bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compensatory Genetic and Transcriptional Cytonuclear Coordination in Allopolyploid Lager Yeast (Saccharomyces pastorianus)
Authors: Zhang Keren , Li Juzuo , Li Guo , Zhao Yue , Dong Yuefan , Zhang Ying , Sun Wenqing , Wang Junsheng , Yao Jinyang , Ma Yiqiao , Wang Hongyan , Zhang Zhibin , Wang Tianya , Xie Kun , Wendel Jonathan F , Liu Bao , Gong Lei 
Published: October 2022

Abstract
Cytonuclear coordination between biparental-nuclear genomes and uniparental-cytoplasmic organellar genomes in plants is often resolved by genetic and transcriptional cytonuclear responses. Whether this mechanism also acts in allopolyploid members of other kingdoms is not clear. Additionally, cytonuclear coordination of interleaved allopolyploid cells/individuals within the same population is underexplored. The yeast Saccharomyces pastorianus provides the opportunity to explore cytonuclear coevolution during different growth stages and from novel dimensions. Using S. pastorianus cells from multiple growth stages in the same environment, we show that nuclear mitochondria-targeted genes have undergone both asymmetric gene conversion and growth stage-specific biased expression favoring genes from the mitochondrial genome donor (Saccharomyces eubayanus). Our results suggest that cytonuclear coordination in allopolyploid lager yeast species entails an orchestrated and compensatory genetic and transcriptional evolutionary regulatory shift. The common as well as unique properties of cytonuclear coordination underlying allopolyploidy between unicellular yeasts and higher plants offers novel insights into mechanisms of cytonuclear evolution associated with allopolyploid speciation.
CREAMMIST: an integrative probabilistic database for cancer drug response prediction
Authors: Yingtaweesittikul Hatairat , Wu Jiaxi , Mongia Aanchal , Peres Rafael , Ko Karrie , Nagarajan Niranjan , Suphavilai Chayaporn 
Published: October 2022

Abstract
Extensive in vitro cancer drug screening datasets have enabled scientists to identify biomarkers and develop machine learning models for predicting drug sensitivity. While most advancements have focused on omics profiles, cancer drug sensitivity scores precalculated by the original sources are often used as-is, without consideration for variabilities between studies. It is well-known that significant inconsistencies exist between the drug sensitivity scores across datasets due to differences in experimental setups and preprocessing methods used to obtain the sensitivity scores. As a result, many studies opt to focus only on a single dataset, leading to underutilization of available data and a limited interpretation of cancer pharmacogenomics analysis. To overcome these caveats, we have developed CREAMMIST (https://creammist.mtms.dev), an integrative database that enables users to obtain an integrative dose-response curve, to capture uncertainty (or high certainty when multiple datasets well align) across five widely used cancer cell-line drug–response datasets. We utilized the Bayesian framework to systematically integrate all available dose-response values across datasets (&gt;14 millions dose-response data points). CREAMMIST provides easy-to-use statistics derived from the integrative dose-response curves for various downstream analyses such as identifying biomarkers, selecting drug concentrations for experiments, and training robust machine learning models.
The Microstructural Record of Convection in the Little Minch Sill Complex, Scotland
Authors: Holness Marian B , Nicoli Gautier , Rust Alison , Neufeld Jerome 
Published: October 2022

Abstract
Detailed microstructural analysis of three basaltic sills of the Little Minch Sill Complex demonstrates that convection leaves a detectable signature in fully solidified bodies. The presence of dense clusters of equant grains of olivine and clinopyroxene in the central parts of sills can only be accounted for if they formed and were enlarged while suspended in convecting magma, with delayed settling to the sill floor. An associated stratigraphic invariance of plagioclase grain shape is consistent with growth while suspended in convecting magma. These microstructural indicators demonstrate that convection during solidification was vigorous and long-lived in the 135-m-thick picrodolerite-crinanite unit (PCU) of the composite Shiant Isles Main sill and vigorous and likely short-lived in the PCU of the composite Creagan Iar sill. In contrast, convection in the Meall Tuath sill was weak and short-lived: plagioclase grain shape in this sill varies with stratigraphic height, indicative of primarily in situ nucleation and growth at the magma-mush interface, while olivine and clinopyroxene were kept suspended in the overlying convecting magma. The magma in all three sills fractionated during solidification, permitting convection driven by the instability of an upper thermal boundary layer. The comparative vigour and longevity of convection in the Shiant Isles Main sill and the Creagan Iar sill was due to their emplacement above an earlier, still-hot, intrusion, resulting in highly asymmetric cooling.
Rüdin’s 1916 Monograph: On the Inheritance and Primary Origin of Dementia Praecox
Authors: Kendler Kenneth S , Klee Astrid 
Published: October 2022

Abstract
In 1916, Ernst Rüdin published the first modern family study in the history of psychiatric genetics, the major goal of which was to test whether the pattern of risk in the siblings of dementia praecox (DP) probands followed Mendelian expectations. He utilized systematic ascertainment of probands and multisourced diagnostic assessments of probands and relatives, applying the narrow Kraepelinian concept of DP. In a novel step, he collaborated closely with a statistical geneticist—Wilhelm Weinberg—and applied his sibling, proband, and age correction methods. In his key sample—701 sibships when neither parent had DP—the morbid risk for DP in siblings was 4.48%, much lower than 25% expected for a recessive disorder. Risk for DP was increased by alcoholism or other mental disorders in parents. Other non-DP psychoses were common in both siblings and parents of DP probands. Rüdin discussed several alternative genetic models for DP including a 2-locus recessive, incomplete penetrance, and an oligogenic model. The high rates of other psychoses and psychopathic personalities in relatives might arise, he suggested, because these disorders shared genetic risks with DP. Rüdin established that DP, when carefully studied, ran in families, did not have a simple Mendelian genetic transmission pattern, and appeared likely to be genetically related to other non-DP psychotic disorders and perhaps some kinds of psychopathic personalities. This study, the most important in Rüdin’s career, should be viewed in the context of his later extensive support of and collaboration with Nazi eugenic policies.
The Beginnings of Scientific Psychiatric Twin Research: Luxenburger’s 1928 “Preliminary Report on the Psychiatric Examination of a Series of Twins”
Authors: Kendler Kenneth S , Klee Astrid 
Published: October 2022

Abstract
While reports of twin pairs concordant for insanity began to appear in the 19th century, the first modern psychiatric twin study that fulfilled Galton’s 1875 promise of the value of the twin method was published by the German Psychiatrist and Geneticist Hans Luxenburger in 1928. Luxenburger introduced four major methodological advances: the use of representative sampling, proband-wise concordance, rigorous zygosity diagnoses, and age correction. He used a narrow Kraepelinian diagnostic approach diagnosis and ascertained twins hospitalized, on a specific day, in all large Bavarian asylums. We include a brief biography of Luxenburger, summarize the findings of his paper and provide a full English translation in the appendix. Luxenburger presents evidence that the frequency of twinning in those with severe mental illness were as expected and reports proband-wise concordance for probable and definite dementia praecox (MZ—76%, DZ—0%) and manic-depressive insanity (MZ—75%, DZ—0%). He also examined eccentricity and hyperthymic or hypothymic personality in the dementia praecox and manic-depressive pairs, respectively. Luxenburger’s substantial contributions to the history of psychiatric genetics should be considered in the context of his intimate but ambivalent relationship with the racial-hygiene policy of the German National Socialists.
Experiences and needs of parents whose child has attempted suicide
Authors: Raney Kayla , Popa Kim , Gallegos Cara 
Published: October 2022

Abstract

Purpose:
To explore the stress, experience, and unmet needs of parents whose child has attempted suicide.

Methods:
A 23-question survey and a 53-item Family Management Measurement questionnaire were distributed to the parents of children admitted to an acute care facility for a suicide attempt (SA). Quantitative data were analyzed using Statistical Analysis System. Responses to the open-ended questions were sorted, synthesized, and clustered into tentative categories.

Results:
Eleven parents enrolled, but only 10 completed the qualitative questions. Three themes emerged: feelings of helplessness, uncertainty, and life management difficulty. Parents rated their stress as moderate (6.6 out of 10). Internal consistency (Cronbach's alpha) was questionable (0.69); however, three of six subscales were good to excellent (0.81-0.95).

Conclusion:
Families experience stress, feelings of hopelessness, and uncertainty after an SA. More research is needed to better understand and quantify parental experiences.
Effect of the Premature Infant Oral Motor Intervention on Sucking Capacity in Preterm Infants in Turkey
Authors: Guler Selver , Cigdem Zerrin , Lessen Knoll Brenda S. , Ortabag Tulay , Yakut Yavuz 
Published: October 2022

Background:
Preterm infants have oral feeding difficulty that often delays discharge, indicating a need for evidence-based interventions for oral–motor development.

Purpose:
To test the Premature Infant Oral Motor Intervention (PIOMI) on the development of oral–motor function, feeding, and anthropometric outcomes using sucking manometry.

Methods:
A single-blind randomized experimental design was conducted with a sample of 60 preterm infants from 2 neonatal intensive care units between May 2019 and March 2020. The experimental group received PIOMI for 5 min/d for 14 consecutive days. Sucking capacity, anthropometrics (weight and head circumference), bottle feeding, breast/chest feeding initiation, and length of hospital stay were measured. The Yakut Sucking Manometer (PCT/TR2019/050678) was developed specifically for this study and tested for the first time.

Results:
The experimental group had a statistically significant percent increase over controls in sucking power (69%), continuous sucking before releasing the bottle (16%), sucking time (13%), and sucking amount (12%) with partial η2 values of interaction between the groups of 0.692, 0.164, 0.136, and 0.121, respectively. The experimental group had a higher increase in weight (89%) and head circumference (81%) over controls (F = 485.130, P < .001; F = 254.754, P < .001, respectively). The experimental group transitioned to oral feeding 9.9 days earlier than controls (t = −2.822; P = .007), started breast/chest feeding 10.8 days earlier (t = 3.016; P = .004), and were discharged 3.0 days earlier.

Implications for Research/Practice:
The PIOMI had a significant positive effect on anthropometrics, sucking capacity, readiness to initiate bottle and breast/chest feeding, and a 3-day reduction in length of hospital stay.
Development of a Mobile Application to Represent Food Intake in Inpatients: Dietary Data Systematization
Authors: Molter ARJO , Brazil PE , Fonseca CF , Bacelo AC 
Published: October 2022

AbstractBackgroundNutritional risk situations related to decreased food intake in the hospital environment hinder nutritional care and increase malnutrition in hospitalized patients and are often associated with increased morbidity and mortality.ObjectiveTo develop and test the reliability of a mobile application as a virtual instrument to assess the acceptability and quality of hospital diets for inpatients.MethodsThis intra- and interobserver development and reliability study investigated an in-hospital food intake monitoring application based on a validated instrument for patients with infectious diseases who were treated at the Evandro Chagas National Institute of Infectious Diseases (INI/FIOCRUZ). The instrument was sequentially administered to patients 48 h after admission to INI hospital units using the printed instrument (paper) and the tested digital application (ARIETI) simultaneously. The tested reliability factor was the consistency of the method in the digital platform, checking whether the application provided equivalent data to the paper instrument, and finally a statistical analysis plan was performed in the R platform version 4.2.0. This project was authorized by the FIOCRUZ/INI Research Ethics Committee under CAAE 35379820.4.0000.5262.ResultsThe ARIETI was developed and tested for reliability in 70 participants, showing similar ability to show caloric intake in Kcal (p = 1.72 E-03), protein intake (g) (p = 0.006362), the proportion of caloric intake (p = 1.54 E-05), and the protein intake (p = 0.003501) relative to the prescribed goal. The application was superior to the paper-based instrument, accelerating the diagnosis of nutritional risk based on food intake by up to 250 s (50–350 min).ConclusionsThe ARIETI optimized the time between diagnosis of nutritional risk related to dietary intake and the nutritionist’s decision making, showing an improved ability to maintain information quality compared to the paper-based instrument.
CORRELATION BETWEEN MEASURED PARAMETERS OF RISK AND PROGNOSIS IN SUBJECTS WITH CHRONIC PERIODONTITIS
Authors: Chandra Rampalli Viswa , Shravan Tulasi 
Published: October 2022

AimsIn most ofcases, clinical parameters associated with poor prognosis are the same as the factors associated with increased risk, but the relationship between risk and prognosis remains unclear.The objective of this study was to evaluate the correlation between measured parameters of predictive risk and prognosisin subjects with chronic periodontitis.Methods300 subjects participated in the study. Modified periodontal risk assessment model (MPRA) was used to assess the risk and prognosis was evaluated by using McGuire and Nunn prognostic criteria.ResultsAmong the subjects, 57.3%, 38% and 4.7% were categorized as having high, low and medium risk respectively. Assessment of prognosis among study subjects showed that 38.0%, 24.0%, 17.7%, 17.0%, 2.0%and1.3% had good, fair, excellent, poor, hopeless and questionable prognosis respectively. Though majority of the subjects had good prognosis (114 subjects;38%), there was a substantial variability in the distribution of the measured parameters as per the risk scores within this cohort. A strong positive correlation was seen between prognosis and probing depth (PD)≥5mm. There was a weak, but statistically significant correlation between predictive risk from MPRA and various types of prognosis(rs=0.507;p<0.001).ConclusionThe measures used to assess risk and prognosis are almost similar;butthe weak correlation between risk and prognosisseems to suggest that an increased risk of developing periodontal disease need notnecessarily indicate a bad prognosis.
Clinical antiviral efficacy of remdesivir and casirivimab/imdevimab against the SARS-CoV-2 Delta and Omicron variants
Authors: Jittamala Podjanee , Schilling William HK , Watson James A , Luvira Viravarn , Siripoon Tanaya , Ngamprasertchai Thundon , Almeida Pedro J , Ekkapongpisit Maneerat , Cruz Cintia , Callery James J , Boyd Simon , Anunsittichai Orawan , Hongsuwan Maliwan , Singhaboot Yutatirat , Pagornrat Watcharee , Tuntipaiboontana Runch , Kruabkontho Varaporn , Ngernseng Thatsanun , Tubprasert Jaruwan , Abdad Mohammad Yazid , Keayarsa Srisuda , Madmanee Wanassanan , Aguiar Renato S , Santos Franciele M , Batty Elizabeth M , Hanboonkunupakarn Pongtorn , Hanboonkunupakarn Borimas , Sookprome Sakol , Poovorawan Kittiyod , Imwong Mallika , Taylor Walter RJ , Chotivanich Vasin , Sangketchon Chunlanee , Ruksakul Wiroj , Chotivanich Kesinee , Pukrittayakamee Sasithon , Dondorp Arjen M , Day Nicholas PJ , Teixeira Mauro M , Piyaphanee Watcharapong , Phumratanaprapin Weerapong , White Nicholas J 
Published: October 2022

BackgroundUncertainty over the therapeutic benefit provided by parenteral remdesivir in COVID-19 has resulted in varying treatment guidelines. Early in the pandemic the monoclonal antibody cocktail, casirivimab/imdevimab, proved highly effective in clinical trials but because of weak or absentin vitroactivity against the SARS-CoV-2 Omicron BA.1 subvariant, it is no longer recommended.MethodsIn a multicenter open label, randomized, controlled adaptive platform trial, low-risk adult patients with early symptomatic COVID-19 were randomized to one of eight treatment arms including intravenous remdesivir (200mg followed by 100mg daily for five days), casirivimab/imdevimab (600mg/600mg), and no study drug. The primary outcome was the viral clearance rate in the modified intention-to-treat population derived from daily log10viral densities (days 0-7) in standardized duplicate oropharyngeal swab eluates. This ongoing adaptive trial is registered atClinicalTrials.gov(NCT05041907).ResultsAcceleration in mean estimated SARS-CoV-2 viral clearance, compared with the contemporaneous no study drug arm (n=64), was 42% (95%CI 18 to 73%) for remdesivir (n=67). Acceleration with casirivimab/imdevimab was 58% (95%CI: 10 to 120) in Delta (n=13), and 20% (95%CI: 3 to 43) in Omicron variant (n=61) infections compared with contemporaneous no study drug arm (n=84). In apost hocsubgroup analysis viral clearance was accelerated by 8% in BA.1 (95%CI: −21 to 59) and 23% (95%CI: 3 to 49) in BA.2 and BA.5 Omicron subvariants.ConclusionsParenteral remdesivir accelerates viral clearance in early symptomatic COVID-19. Despite substantially reducedin vitroactivities, casirivimab/imdevimab retainsin vivoantiviral activity against COVID-19 infections caused by currently prevalent Omicron subvariants.Brief summaryIn early symptomatic COVID-19 remdesivir accelerated viral clearance by 42% while the monoclonal antibody cocktail casirivimab/imdevimab accelerated clearance by approximately 60% in SARS-CoV-2 Delta variant infections, and by approximately 25% in infections with Omicron subvariants BA.2 and BA.5.
Single-cell molecular profiling using ex vivo functional readouts fuels precision oncology in glioblastoma
Authors: Panovska Dena , Nazari Pouya , Cole Basiel , Creemers Pieter-Jan , Derweduwe Marleen , Solie Lien , Gassen Sofie Van , Claeys Annelies , Verbeke Tatjana , Saeys Yvan , Van Der Plancken David , Bosisio Francesca M. , Put Eric , Bamps Sven , Clement Paul M. , Verfaillie Michiel , Sciot Raf , Ligon Keith L. , Vleeschouwer Steven De , Antoranz Asier , Smet Frederik De 
Published: October 2022

AbstractBackgroundFunctional profiling of freshly isolated glioblastoma cells is being evaluated as a next-generation method for precision oncology. While promising, its success largely depends on the method to evaluate treatment activity which requires sufficient resolution and specificity.MethodsHere, we describe the ‘precisiononcology bysingle-cellprofiling usingex vivoreadouts of functionality’ (PROSPERO) assay to evaluate the intrinsic susceptibility of high- grade brain tumor cells to respond to therapy. Different from other assays, PROSPERO extends beyond life/death screening by rapidly evaluating acute molecular drug responses at single-cell resolution.ResultsThe PROSPERO assay was developed by correlating short-term single-cell molecular signatures using CyTOF to long-term cytotoxicity readouts in representative patient- derived glioblastoma cell cultures (n=14) that were exposed to radiotherapy and the small- molecule p53/MDM2 inhibitor AMG232. The predictive model was subsequently projected to evaluate drug activity in freshly resected GBM samples from patients (n=34).Here,PROSPERO revealed an overall limited capacity of tumor cells to respond to therapy, as reflected by the inability to induce key molecular markers uponex vivotreatment exposure, while retaining proliferative capacity, insights that were validated in PDX models. This approach also allowed the investigation of cellular plasticity, which in PDCLs highlighted therapy-induced proneural-to-mesenchymal transitions, while in patients’ samples this was more heterogeneous.ConclusionPROSPERO provides a precise way to evaluate therapy efficacy by measuring molecular drug responses using specific biomarker changes in freshly resected brain tumor samples, in addition to providing key functional insights in cellular behavior, which may ultimately complement standard, clinical biomarker evaluations.
In vitromodelling of oral microbial invasion in the human colon
Authors: Etienne-Mesmin Lucie , Meslier Victoria , Uriot Ophélie , Fournier Elora , Deschamps Charlotte , Denis Sylvain , David Aymeric , Jegou Sarah , Morabito Christian , Quinquis Benoit , Thirion Florence , Oñate Florian Plaza , Le Chatelier Emmanuelle , Ehrlich S. Dusko , Blanquet-Diot Stéphanie , Almeida Mathieu 
Published: October 2022

ABSTRACTRecent advances in the human microbiome characterization have revealed significant oral microbial detection in stools of dysbiotic patients. However, little is known about the potential interactions of these invasive oral microorganisms with commensal intestinal microbiota and host. In this proof of concept study, we propose a new model of oral to gut invasion by the combined use of anin vitromodel simulating both the physicochemical and microbial (lumen and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol and whole metagenome shotgun sequencing. Oral invasion of the intestinal microbiota was simulated by injection of enriched saliva in thein vitrocolon model inoculated with faecal sample from the same healthy adult donor. The mucosal compartment of M-ARCOL was able to retain the highest species richness levels over time, whilst it decreased in the luminal compartment. This study also showed that oral microorganisms preferably colonized the mucosal microenvironment, suggesting potential oral-to-intestinal mucosal competitions. This new model of oral-to-gut invasion can provide useful mechanistic insights into the role of oral microbiome in various disease processes.