Phylotranscriptomic discordance is best explained by incomplete lineage sorting within Allium subgenus Cyathophora and thus hemiplasy accounts for interspecific trait transition

The transition of traits between genetically related lineages is a fascinating topic that provides clues to understanding the drivers of speciation and diversification.Much can be learned about this process from phylogeny-based trait evolution.However,such inference is often plagued by genome-wide gene-tree discordance(GTD),mostly due to incomplete lineage sorting(ILS)and/or introgressive hybridization,especially when the genes underlying the traits appear discordant.Here,by collecting transcriptomes,whole chloroplast genomes(cpDNA),and population genetic datasets,we used the coalescent model to turn GTD into a source of information for ILS and employed hemiplasy to explain specific cases of apparent“phylogenetic discordance”between different morphological traits and probable species phylogeny in the Allium subg.Cyathophora.Both concatenation and coalescence methods consistently showed the same phylogenetic topology for species tree inference based on single-copy genes(SCGs),as supported by the KS distribution.However,GTD was high across the genomes of subg.Cyathophora:~27%e38.9%of the SCG trees were in conflict with the species tree.Plasmid and nuclear incongruence was also present.Our coalescent simulations indicated that such GTD was mainly a product of ILS.Our hemiplasy risk factor calculations supported that random fixation of ancient polymorphisms in different populations during successive speciation events along the subg.Cyathophora phylogeny may have caused the character transition,as well as the anomalous cpDNA tree.Our study exemplifies how phylogenetic noise can be transformed into evolutionary information for understanding character state transitions along species phylogenies.

Immunovirological Discordance and Associated Factors among People Living with HIV under Antiretroviral Treatment at Hôpital de Jour de Donka, Guinea

The antiretroviral treatment (ART) has significantly reduced the number of new HIV/AIDS infections and related deaths. However, cases of immunovirological discordance (IVD) are found in various locations. The objective of this study was to determine the profile of People living with HIV (PLHIV) with IVD and to identify associated factors. We conducted a cross-sectional study based on the records of PLHIV under ART for at least 6 months, followed at Hpital de Jour Donka from 2015 to 2017, and having both viral load (CV) and CD4 T-cell count. Prevalence of IVD was 34.57%, with 23.87% for immunological discordance (ID) and 10.7% for virological discordance (VD). Females were predominant (66.26%), and male gender influenced IVD with a statistically significant difference (p = 0.006) and was associated with VD (p = 0.007). The average age was 38.77 11.30 years. PLHIV were classified at WHO stages 3 and 4 (86.01%). The median initial haemoglobin level was 11.5 g/L [3.2 - 12]. The mean initial CD4 T-cell count was 272.84 cells/mm3 201.6. The median initial viral load (VL) was 147,337 copies/mL [1092 - 31,675,000]. The initial CD4 T-cell count 3 was associated with IVD with a statistically significant difference (p = 0.0009) and correlated with ID (p = 0.000). Prurigo was associated with IVD with a statistically significant difference (p = 0.003). Cerebral toxoplasmosis was not associated with IVD but was associated with ID (p = 0.04). This study allowed us to describe the profile of PLHIV with IVD. The main associated factors were male gender, initial CD4 T-cell count 3, toxoplasmosis, prurigo, and herpes zoster.

Influence of bed elevation discordance on flow patterns and head losses in an open-channel confluence

Confluences play a major role in the dynamics of networks of natural and man-made open channels, and field measurements on river confluences reveal that discordance in bed elevation is common.Studies of schematized confluences with a step at the interface between the tributary and the main channel bed reveal that bed elevation discordance is an important additional control for the confluence hydrodynamics.This study aimed to improve understanding of the influence of bed elevation discordance on the flow patterns and head losses in a right-angled confluence of an open channel with rectangular cross-sections.A large eddy simulation (LES)-based numerical model was set up and validated with experiments by others.Four configurations with different bed discordance ratios were investigated.The results confirm that, with increasing bed elevation discordance, the tributary streamlines at the confluence interface deviate less from the geometrical confluence angle, the extent of the recirculation zone (RZ) gets smaller, the ratio of the water depth upstream to that downstream of the confluence decreases, and the water level depression reduces.The bed elevation discordance also leads to the development of a large-scale structure in the lee of the step.Despite the appearance of the large-scale structure, the reduced extent of the RZ and associated changes in flow deflection/contraction reduce total head losses experienced by the main channel with an increase of the bed discordance ratio.It turns out that bed elevation discordance converts the lateral momentum from the tributary to streamwise momentum in the main channel more efficiently.

HER2 discordance between paired primary gastric cancer and metastasis:a meta-analysis

Background： A number of studies have examined human epidermal growth factor receptor 2 （HER2） status in primary gastric cancer （GC） and associated metastasis, some showed their great concordance in FIER2 expression, but others demonstrated notable discordance. There is still little consensus on HER2 discordance, therefore, a systematic review and meta-analysis was conducted to assess the status on HER2 discordance between primary GC and its paired metastasis. Methods： PubMed, EMBASE, ASCO and The Cochrane Library were searched for studies that explored the concordance between primary tumor and metastasis in patients with GC up to 10 March, 2014. Data of discordance of HER2 between primary GC and corresponding metastasis were extracted from the publications and random-effects models were used to estimate pooled discordance proportions. Results： Eighteen articles including 1,867 patients were included for the meta-analysis in accordance with the selection criteria. Pooled discordance proportions were 7% [95% confidence interval （CI）： 5-10%] for HER2 status. Pooled proportions of tumors shifting from positive to negative and from negative to positive were 17% （95% CI： 7-29%） and 4% （95% CI： 2-6%） respectively. No publication bias was found in the meta-analysis. Conclusions： The discordance of HER2 status is not rare in primary and metastatic GC through our metaanalysis. Prospective studies are needed to testify the clinical significance of the discordance of HER2 status.

Rapid genetic divergence and mitonuclear discordance in the Taliang knobby newt(Liangshantriton taliangensis,Salamandridae,Caudata)and their driving forces

The Hengduan Mountains Region(HMR)is the largest“evolutionary frontier”of the northern temperate zone,and the origin and maintenance of species in this area is a research hotspot.Exploring species-specific responses to historical and contemporary environmental changes will improve our understanding of the role of this region in maintaining biodiversity.In this study,mitochondrial and microsatellite diversities were used to assess the contributions of paleogeological events,Pleistocene climatic oscillations,and contemporary landscape characteristics to the rapid intraspecific diversification of Liangshantriton taliangensis,a vulnerable amphibian species endemic to several sky-island mountains in the southeastern HMR.Divergence date estimations suggested that the East Asian monsoon,local uplifting events(Xigeda Formation strata),and Early-Middle Pleistocene transition(EMPT)promoted rapid divergence of L.taliangensis during the Pleistocene,yielding eight mitochondrial lineages and six nuclear genetic lineages.Moreover,population genetic structures were mainly fixed through isolation by resistance.Multiple in situ refugia were identified by ecological niche models and high genetic diversity,which played crucial roles in the persistence and divergence of L.taliangensis during glacial-interglacial cycles.Dramatic climatic fluctuations further promoted recurrent isolation and admixing of populations in scattered glacial refugia.The apparent mitonuclear discordance was likely the result of introgression by secondary contact and/or female-biased dispersal.Postglacial expansion generated two major secondary contact zones(Ganluo(GL)and Chuhongjue(CHJ)).Identification of conservation management units and dispersal corridors offers important recommendations for the conservation of this species.

Large along-axis variations in magma supply and tectonism of the Southeast Indian Ridge near the Australian-Antarctic Discordance

We analyzed seafloor morphology and geophysical anomalies of the Southeast Indian Ridge(SEIR) to reveal the remarkable changes in magma supply along this intermediate fast-spreading ridge. We found systematic differences of the Australian-Antarctic Discordance(AAD) from adjacent ridge segments with the residual mantle Bouguer gravity anomaly(RMBA) being more positive, seafloor being deeper, morphology being more chaotic, M factors being smaller at the AAD. These systematic anomalies, as well as the observed Na8.0 being greater and Fe8.0 being smaller at AAD, suggest relatively starved magma supply and relatively thin crust within the AAD.Comparing to the adjacent ridges segments, the calculated average map-view M factors are relatively small for the AAD, where several Oceanic Core Complexes(OCCs) develop. Close to 30 OCCs were found to be distributed asymmetrically along the SEIR with 60% of OCCs at the northern flank. The OCCs are concentrated mainly in Segments B3 and B4 within the AAD at ~124°–126°E, as well as at the eastern end of Zone C at ~115°E. The relatively small map-view M factors within the AAD indicate stronger tectonism than the adjacent SEIR segments.The interaction between the westward migrating Pacific mantle and the relatively cold mantle beneath the AAD may have caused a reduction in magma supply, leading to the development of abundant OCCs.

Decomposition of Independence Using the Logit Uniform Association Model and Equality of Concordance and Discordance for Two-Way Classifications

For two-way contingency tables with ordered categories, the present paper gives a theorem that the independence model holds if and only if the logit uniform association model holds and equality of concordance and discordance for all pairs of adjacent rows and all dichotomous collapsing of the columns holds. Using the theorem, we analyze the cross-classification of duodenal ulcer patients according to operation and dumping severity.

Double Discordance with Pulmonary Stenosis: About a Clinical Case

Introduction: Double discordance or corrected transposition of the great vessels is a rare congenital heart disease. It is an atrioventricular and ventriculo-arterial mismatch. It is a complex and unusual form of congenital heart disease. Often asymptomatic, in its isolated form, bradycardia, murmur and cyanosis can be a mode of revelation. Case presentation: We report the case of an 11-year-old child, asymptomatic at birth, after he started to have dyspnea on exertion, recurrent bronchitis, motivating a cardiological consultation. On cardiac physical examination, the heart sounds regular, not rapid at 81 BPM with a grade 3-4/6 systolic murmur at the 4th left EIC (Intercostal space). EKG (electrocardiogram) shows PR interval at 0.20 seconds. Cardiac ultrasound reveals atrioventricular discordance, vascular malposition, anterior aorta, the two vessels placed side by side, minimal pulmonary insufficiency, a small leak at the levels of the mitral and tricuspid valves, dystrophic pulmonary valves with an average gradient of 91 mmHg, max at 158 mmHg. Regular follow-up has been recommended through the performance of a clinical examination and cardiac ultrasound. Conclusion: The double discordance can be asymptomatic, and survival can be long in the isolated forms, but the evolution is not always benign, especially in the associated forms. It depends on the function of the systemic right ventricle and associated abnormalities.

Phylogenomic cytonuclear discordance and evolutionary histories of plants and animals

The field of evolutionary biology has been revolutionized by phylogenomic approaches in the last decades. However, with the ever-increasing size and scope of molecular data collection, conflicting genealogies may be yielded based on different datasets and analytical approaches, a phenomenon known as cytonuclear discordance(Figure 1A and B).

Retrospective analysis of discordant results between histology and other clinical diagnostic tests on helicobacter pylori infection

BACKGROUND A reliable test is essential for diagnosing Helicobacter pylori(H.pylori)infection,and crucial for managing H.pylori-related diseases.Serving as an excellent method for detecting H.pylori infection,histologic examination is a test that clinicians heavily rely on,especially when complemented with immunohistochemistry(IHC).Additionally,other diagnostic tests for H.pylori,such as the rapid urease test(CLO test)and stool antigen test(SA),are also highly sensitive and specific.Typically,the results of histology and other tests align with each other.However,on rare occasions,discrepancy between histopathology and other H.pylori diagnostic tests occurs.AIM To investigate the discordance between histology and other H.pylori tests,the underlying causes,and the impact on clinical management.METHODS Pathology reports of gastric biopsies were retrieved spanning August 2013 and July 2018.Reports were included in the study only if there were other H.pylori tests within seven days of the biopsy.These additional tests include CLO test,SA,and H.pylori culture.Concordance between histopathology and other tests was determined based on the consistency of results.In instances where histology results were negative while other tests were positive,the slides were retrieved for re-assessment,and the clinical chart was reviewed.RESULTS Of 1396 pathology reports were identified,each accompanied by one additional H.pylori test.The concordance rates in detecting H.pylori infection between biopsy and other tests did not exhibit significant differences based on the number of biopsy fragments.117 discrepant cases were identified.Only 20 cases(9 with CLO test and 11 with SA)had negative biopsy but positive results in other tests.Four cases initially stained with Warthin-Starry turned out to be positive for H.pylori with subsequent IHC staining.Among the remaining 16 true discrepant cases,10 patients were on proton pump inhibitors before the biopsy and/or other tests.Most patients underwent treatment,except for two who were untreated,and two patients who were lost to follow-up.CONCLUSION There are rare discrepant cases with negative biopsy but positive in SA or CLO test.Various factors may contribute to this inconsistency.Most patients in such cases had undergone treatment.

Quantum discord and its dynamics for multipartite systems

Quantum discord, one of the famous quantum correlations, has been recently generalized to multipartite systems by Radhakrishnan et al. Here we give analytical solutions of the quantum discord for a family of N-qubit quantum states. For the bipartite system, we derive a zero quantum discord which will remain unchanged under the phase damping channel. For multiparitite systems, it is found that the quantum discord can be classified into three categories and the quantum discord for odd-partite systems can exhibit freezing under the phase damping channel, while the freezing does not exist in the even-partite systems.

国际传播中虚拟文娱的多维效用与认知形塑机制——基于Discord的LDA实证研究

虚拟文娱是借助虚拟现实技术而实现,在感觉维度上存在的文化娱乐形态。从全球性社交平台Discord中收集Pico社区的讨论数据,使用LDA主题分析与情感分析方法研究发现,虚拟文娱依托具身传播推进感官交织,通过促进交流升维凝聚社会性共识,构建起虚实融合的超越性场域,由此建立“自我—社群—场域”的认知形塑机制,从而影响海外民众对中国形象的认知。虚拟文娱在接触海外Z世代群体、传递国家形象、开辟全球性交流空间中具有较大潜力。

THREE-DIMENSIONAL SIMULATION FOR EFFECTS OF BED DISCORDANCE ON FLOW DYNAMICS AT Y-SHAPED OPEN CHANNEL CONFLUENCES

Channel confluences are universally present in nature. They can be divided into two types： asymmetrical river confluences and symmetric river confluences. The latter is also called as the Y-shaped confluences. Most of previous work has paid more attention to the asymmetrical river confluences, but few studies have been conducted on the Y-shaped confluences. In this article, the effects of bed discordance on the flow patterns at ＂Y＂ shaped open-channel confluences were studied by using a 3-D numerical simulation. It is proved that the model can undertake quantitative assessment of the flow at confluences. The results indicate that there are a lot of differences between the Y-shaped confluence and asymmetrical confluence. The discordant bed height plays an important role at the Y-shaped junction.

A wide hybrid zone mediated by precipitation contributed to confused geographical structure of Scutiger boulengeri

Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology.In this study,we generated a time-calibrated phylogeny of Scutiger boulengeri,an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang(Tibet)Plateau(QTP).Based on three mitochondrial DNA(mt DNA)genes,eight clades were assigned to three deeply divergent lineages.Analysis of nuclear DNA(nu DNA)genes revealed three distinct clusters without geographic structure,indicating significantly high rates of gene flow.Coalescent theory framework analysis(approximate Bayesian computation model DIYABC and Migrate-N)suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago(Ma).The ratio of mt DNA FST(fixation index)to nu DNA FST was 2.3,thus failing to show male-biased dispersal.Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China,without significant reproductive isolation but with strong introgression in S.boulengeri,suggesting high hybrid fitness.Furthermore,mt DNA genes exhibited isolation by distance(IBD)while nu DNA genes exhibited significant isolation by environment(IBE).Results suggested that mitonuclear discordance may have initially been caused by geographic isolation,followed by precipitation-mediated hybridization,producing a wide hybrid zone and geographic structure confusion of nu DNA genes in S.boulengeri.This study indicated that complicated historical processes may have led to specific genetic patterns,with a specific climate factor facilitating gene flow in the system.

Discrepancy among microsatellite instability detection methodologies in non-colorectal cancer:Report of 3 cases

BACKGROUND Microsatellite instability(MSI)is a predictive biomarker for cancer immunotherapy.The tumor-agnostic nature of MSI makes it a denominator for immunotherapy in several solid tumors.It can be assessed using next-generation sequencing(NGS),fluorescent multiplex PCR,and immunohistochemistry(IHC).CASE SUMMARY Here,we report 3 cases with discordant MSI results detected using different methods.A cholangiocellular carcinoma case revealed proficient mismatch repair(MMR)by IHC but high MSI(MSI-H)by liquid NGS.A cervical cancer case revealed deficient MMR by IHC,microsatellite stable by PCR,and MSI-H by NGS.Lastly,an endometrial cancer case revealed proficient MMR by IHC but MSI-H by NGS.CONCLUSION IHC for MMR status is the first choice due to several advantages.However,in cases of indeterminate IHC results,molecular testing by MSI-PCR is preferred.Recently,NGS-based MSI assays are being widely used to detect MSI-H tumors.All three methods have high accuracy;however,the inconsistencies between them may lead to misdiagnosis.

Egg recognition and nestling discrimination in the Crested Myna(Acridotheres cristatellus):Size matters

Most studies exploring abilities of hosts to detect brood parasitism are based on detecting colour and/or pattern differences among parasitic and host eggs or nestlings,while only few were focused on size differences.True recognition and recognition by discordancy are used to explain cognitive mechanisms of host egg recognition;however,only a few studies have found that hosts use recognition by discordancy.This study investigated:1)whether egg and nestling recognitions in the Crested Myna(Acridotheres cristatellus) are based on size cues;2)whether the egg cognitive mechanism is recognition by discordancy based on size cues;and 3) whether the longer the experiment time,the higher the egg recognition rate.Our results showed that the Crested Myna uses egg or nestling size as a recognition cue while the egg and nestling colour and patterning are not associated with egg or nestling rejection,thus the cognitive mechanism of egg recognition in the Crested Myna is recognition by discordancy based on egg size cues.Furthermore,there is a rejection delay in time of egg rejection behaviour of the Crested Myna.Therefore,we suggest that the periodicity of egg rejection experiments could be appropriately extended,especially for species with relatively low egg recognition ability.

Geometric discord of tripartite quantum systems

We study the quantification of geometric discord for tripartite quantum systems.Firstly,we obtain the analytic formula of geometric discord for tripartite pure states.It is already known that the geometric discord of pure states reduces to the geometric entanglement in bipartite systems,the results presented here show that this property is no longer true in tripartite systems.Furthermore,we provide an operational meaning for tripartite geometric discord by linking it to quantum state discrimination,that is,we prove that the geometric discord of tripartite states is equal to the minimum error probability to discriminate a set of quantum states with von Neumann measurement.Lastly,we calculate the geometric discord of three-qubit Bell diagonal states and then investigate the dynamic behavior of tripartite geometric discord under local decoherence.It is interesting that the frozen phenomenon exists for geometric discord in this scenario.

Profile of Discordant Couples for Human Immunodeficiency Virus Infection Followed in Kinshasa: Case of Monkole Medical Center

Background: Programs targeting serodiscordant couples in Africa are not a priority in efforts to prevent Human Immunodeficiency Virus (HIV) infection, although a large proportion of these occur in stable relationships, of which serodiscordance accounts for about two-thirds with a high risk of seroconversion of the seronegative partner. Objective: The objective of this study was to describe the profile of HIV serodiscordant couples followed in Kinshasa, DRC. Methods: Descriptive cross-sectional study to describe the profile of different heterosexual HIV serodiscordant couples followed at the Monkole Medical Center in Kinshasa, DRC, from November 2021 to June 2022. The data were collected from the information sheets elaborated by the research team as well as from the information provided by the computerized files of the patients managed at the Infectious Diseases Unit of the Monkole Medical Center after the signature of the informed consent. An average of 8 cc of blood was taken from a peripheral vein in the patient’s forearm, and was stored in EDTA tubes at −20˚C, of which at least 6 mL were used for biochemical analyses, 2 spots of 200 μL for each partner were stored on filter paper at −20˚C and were used for DNA extraction. Nested PCR confirmed the serological diagnosis. Results: Out of a total of 482 heterosexual couples followed for HIV at the Monkole Medical Center, 28 (5.8%) were HIV serodiscordant, of which 14 (2.9%) couples agreed to participate in the present study. The mean age was 43.39 ± 10 years with extremes ranging from 24 to 62 years. The patients were mainly from the informal sector (53.6%) and weighed between 61 and 71 kg (46.4%). Sexual intercourse continued in all couples, without condom use (85.7%) for desire of procreation (82.1%);although the great majority of HIV-negative partners (85.7%) were not under ARV prophylaxis. Leukopenia was found in 42.9% of HIV-negative partners compared to 21% of HIV-positive partners;all partners had a predominantly lymphocytic white blood cell count. 21.4% of HIV-negative partners had high HDL, 14.3% of HIV-positive partners had low HDL, and 14.3% of HIV-negative partners had high LDL. Chi-square and Pearson correlation tests showed no relationship between the biochemical parameters performed and the couples’ serodiscordance for HIV. Conclusion: The frequency of HIV discordant couples in Kinshasa is significant. Serodiscordance is encountered in young intellectual and entrepreneurial couples with a desire to procreate. It is desirable to carry out further analyses for better management of these couples.

Discordance between chromatin accessibility and transcriptional activity during the human primed-to-naïve pluripotency transition process

Naive pluripotent state can be obtained by several strategies from various types of cells,in which the cell fate roadmap as well as key biological events involved in the journey have been described in detail.Here,we carefully explored the chromatin accessibility dynamics during the primed-to-naïve transition by adopting a dual fluorescent reporter system and the assay for transposase-accessible chromatin(ATAC)-seq.Our results revealed critical chromatin remodeling events and highlight the discordance between chromatin accessibility and transcriptional activity.We further demonstrate that the differential epigenetic modifications and transcription factor(TF)activities may play a critical role in regulating gene expression,and account for the observed variations in gene expression despite similar chromatin landscapes.

Current understandings of the pathogenesis of type 1 diabetes:Genetics to environment

Type 1 diabetes(T1D)is an autoimmune disease that usually strikes early in life,but can affect individuals at almost any age.It is caused by autoreactive T cells that destroy insulin-producing beta cells in the pancreas.Epidemiological studies estimate a prevalence of 1 in 300 children in the United States with an increasing incidence of 2%-5%annually worldwide.The daily responsibility,clinical management,and vigilance required to maintain blood sugar levels within normal range and avoid acute complications(hypoglycemic episodes and diabetic ketoacidosis)and long term micro-and macro-vascular complications significantly affects quality of life and public health care costs.Given the expansive impact of T1D,research work has accelerated and T1D has been intensively investigated with the focus to better understand,manage and cure this condition.Many advances have been made in the past decades in this regard,but key questions remain as to why certain people develop T1D,but not others,with the glaring example of discordant disease incidence among monozygotic twins.In this review,we discuss the field’s current understanding of its pathophysiology and the role of genetics and environment on the development of T1D.We examine the potential implications of these findings with an emphasis on T1D inheritance patterns,twin studies,and disease prevention.Through a better understanding of this process,interventions can be developed to prevent or halt it at early stages.