bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carpal Tunnel Syndrome as a Test Case for Value Assessment During the Presurgical Period
Authors: Sears Erika D. , Evans Richard , Burns Jennifer , Chung Kevin C. , Hayward Rodney A. , Kerr Eve A. 
Published: December 2022

Background:
Few performance measures assess presurgical value (quality and utilization).

Objectives:
Using carpal tunnel syndrome (CTS) as a case study: (1) develop a model to evaluate presurgical quality and utilization and (2) identify opportunities for value improvement.

Research Design:
A retrospective cohort study utilizing Veterans Affairs (VA) national administrative data.

Subjects:
Patients who were evaluated in a VA primary care clinic on at least 1 occasion for CTS and received carpal tunnel release over a 7-year period.

Measures:
We modeled facility-level performance on 2 outcomes: surgical delay (marker of quality) and number of presurgical encounters (utilization) for CTS, and examined association between patient, facility, and care process variables and performance.

Results:
Among 41,912 Veterans undergoing carpal tunnel release at 127 VA medical centers, the median facility-level predicted probability of surgical delay was 48%, with 16 (13%) facilities having significantly less delay than the median and 13 (10%) facilities having greater delay. The median facility-level predicted number of presurgical encounters was 8.8 visits, with 22 (17%) facilities having significantly fewer encounters and 22 (17%) facilities having more. Care processes had a stronger association with both outcomes than structural variables included in the models. Processes associated with the greatest deviations in predicted delay and utilization included receipt of repeat electrodiagnostic testing, use of 2 or more nonoperative treatments, and community referral outside of VA.

Conclusions:
Using CTS as a test case, this study demonstrates the potential to assess presurgical value and identify modifiable care processes associated with presurgical delay and utilization performance.
The Hematology Cancer Patient Experience of “Facing Death” in the Last Year of Life
Authors: Campbell Karen , Harris Fiona , Stoddart Kathleen 
Published: December 2022

Background
For hematology cancer patients, the process of dying is described as “troublesome.” Qualitative studies have focused on views of healthcare professionals and caregiver stakeholders. To date, there have been no studies from the patient’s perspective on facing death while in the last year of life.

Objective
The aim of this study was to develop an understanding of the hematology cancer patient’s experience of the process of dying in the last year of life.

Methods
The study method was constructivist grounded theory using semistructured interviews, a constant comparison technique, and memoing to collection and analysis of data. The 21 participants were attending a UK cancer center, a cancer unit, or a hospice.

Results
This article describes 1 core category within the incurable hematology cancer illness trajectory through 4 subcategories: transitional phase, chronic phase, dying phase, and liminal phase.

Conclusion
This unique study illustrates that, although life can be prolonged, “facing death” still occurs upon hospitalization and relapse regularly over the illness trajectory.

Implications for Practice
It is important that clinical practice acknowledges those participants in an incurable illness trajectory while living are focused on avoiding death rather than the ability to cure the disease. Services need to be responsive to the ambiguity of both living and dying by providing holistic management simultaneously, especially after critical episodes of care, to enhance the process of care in the last year of life, and assessment should incorporate the discussion of experiencing life-threatening events.
Kidney-transplanted Adolescents—Nonadherence and Graft Outcomes During the Transition Phase: A Nationwide Analysis, 2000–2020
Authors: Kindem Ingvild A. , Bjerre Anna , Hammarstrøm Clara , Naper Christian , Midtvedt Karsten , Åsberg Anders 
Published: December 2022

Background.
The transition from pediatric to young adult care is a vulnerable period for the renal transplant patient. We aimed to identify medication nonadherence (noninitiation, nonimplementation, and nonpersistence) and graft loss rates among adolescents and young adults and elucidate the influence of the transition phase on transplant outcomes.

Methods.
A retrospective nationwide cohort analysis of all renal transplantations in Norway from 2000 to 2020 was performed. Data were retrieved from the Norwegian Renal Registry, and adherence data from hospital charts. Patients transplanted aged <50 y, with functioning graft at 6 mo, were included. Recipients transplanted aged <26 y were compared with recipients transplanted aged 26–50 y. Graft loss, acute rejection, and development of de novo donor-specific antibodies were assessed in relation to the transition phase, defined as 14–26 y.

Results.
Data from 1830 kidney recipients were included: 371 (20%) transplanted <26 y (64% male, 68% living donor) versus 1459 transplanted 26–50 y (63% male, 44% living donor). There were 298 graft losses, 78 (21%) in the <26-y group versus 220 (15%) in the 26- to 50-y group. During the transition phase, 36 grafts were lost, 29 (81%) after transfer to the adult service. Medication nonadherence was the reason for 58% (21 of 36) of the losses during the transition phase, versus 12% (27 of 220) in the 26- to 50-y group (P < 0.001). The 5-y graft survival rate was 89% (95% confidence interval, 85%-92%) and 94% (92%-95%), respectively (P = 0.01).

Conclusions.
Nonadherence was verified as the main cause of kidney graft loss in the transition phase.
Selective IgA2deficiency in a patient with small intestinal Crohn’s disease
Authors: Canales-Herrerias Pablo , Garcia-Carmona Yolanda , Meringer Hadar , Martinez-Delgado Gustavo , Tankelevich Michael , Colombel Jean-Frederic , Cunningham-Rundles Charlotte , Cerutti Andrea , Mehandru Saurabh 
Published: December 2022

AbstractThe human IgA response is composed of two structurally different subclasses termed IgA1and IgA2. Compared to IgA1, IgA2has a shorter hinge region, which makes it more resistant to bacterial proteases. IgA1is produced both systemically and in mucosal surfaces, whereas IgA2is mostly confined to the intestines. While the overall IgA response is known to be involved in intestinal homeostasis, the specific contribution of IgA1and IgA2remains largely unknown (Chen 2020). Selective IgA deficiency (SIgAD) is the most prevalent primary immune deficiency. About half of SIgAD cases are associated with heterogeneous but generally mild clinical manifestations. Anecdotal evidence of IgA2deficiency is available (van Loghem 1983, Ozawa 1986, Engström 1990), however no associations with clinical manifestations have been reported.Here, we describe the occurrence of a selective IgA2deficiency in a patient (CD068) with small intestinal Crohn’s disease (CD). The patient had undetectable IgA2+cells and secreted IgA2antibody in both intestine and circulation. Among other features, patient CD068 presented with duodenal and ileal inflammation. To our knowledge, this is the first case of IgA2deficiency with a potential link to IBD, which might shed new insights into potential IgA2-specific functions.
Long-Term Ecological Responses of a Dipterocarp Forest to Climate Changes and Nutrient Availability
Authors: Prohaska Ana , Seddon Alistair W.R. , Rach Oliver , Smith Andrew , Sachse Dirk , Willis Katherine J. 
Published: December 2022

SummaryUnderstanding the long-term impact of projected climate change on tropical rainforests is critical given their central role in the Earth’s system. Palaeoecological records can provide a valuable perspective on this problem. Here we examine for the first time the effects of past climatic changes on the dominant forest type of Southeast Asia – Dipterocarp forest.We use a range of proxies extracted from a 1,400-year-old lacustrine sedimentary sequence from north-eastern Philippines to model long-term vegetation responses of Dipterocarp forest, including its dominant tree group Dipterocarps, to changes in precipitation, fire and nutrient availability over time.Our results show a positive relationship between Dipterocarps pollen accumulation rates (PARs) and leaf wax hydrogen isotope values, which suggests a negative effect of drier conditions on Dipterocarp tree abundance. Furthermore, we find a positive relationship between Dipterocarp PARs and the proxy for phosphorus availability, which suggests phosphorus controls the productivity of these keystone trees on longer time scales. Other plant taxa show widely varying relationships with the abiotic factors, demonstrating a high diversity of functional responses.Our findings provide novel insights into Dipterocarp forest responses to changing climatic conditions in the past, and highlight potential impacts of future climate change on this globally important ecosystem.
Nationwide assessment of leadership development for graduate students in the agricultural plant sciences
Authors: Da Silva Karen Ferreira , Burnham Ella , Louis Joe , Golick Douglas , Everhart Sydney 
Published: December 2022

AbstractLeadership development is a universally important goal across the agricultural plant science disciplines. Although previous studies have identified a need for leadership skills, less is known about leadership skill development in graduate programs. To address this, we constructed a mixed-method study to identify the most significant graduate school leadership experiences of scientists in the agricultural plant science disciplines. The survey was deployed to 6,728 people in the U.S. and received 1,086 responses (16.1% response rate). The majority of respondents reported that they were from one of the major agricultural states and employed at one of the agricultural plant science related doctoral universities, industries, or government. Results from this survey suggest that recent graduates were more engaged in graduate school activities that offered leadership development. Key experiences in graduate school were also identified that may be used to develop future leaders. Additionally, respondents reported the greatest barrier to providing leadership development for graduate students was that it is not part of their program curriculum, however current graduate students responded differently, and identifying lack of funding to support experiences as the greatest barrier. This survey also identified the top ranked professional skills considered most important for effective leaders in agricultural plant sciences as well as respondent-driven recommendations on how graduate programs can improve leadership development. Collectively, these results can be used in the future to identify priorities for skill development and opportunities for graduate student training in leadership skills within the plant science disciplines.
Investigating the outcomes of virus coinfection within and across host species
Authors: Imrie Ryan M. , Walsh Sarah K. , Roberts Katherine E , Lello Joanne , Longdon Ben 
Published: December 2022

AbstractInteractions between coinfecting pathogens have the potential to alter the course of infection and can act as a source of phenotypic variation in susceptibility between hosts. This phenotypic variation may influence the evolution of host-pathogen interactions within host species and interfere with patterns in the outcomes of infection across host species. Here, we examine experimental coinfections of twoCripaviruses– Cricket Paralysis Virus (CrPV), and Drosophila C Virus (DCV) –across a panel of 25Drosophila melanogasterinbred lines and 47Drosophilidaehost species. We find that interactions between these viruses alter viral loads acrossD. melanogastergenotypes, with a ~3 fold increase in the viral load of DCV and a ~2.5 fold decrease in CrPV in coinfection compared to single infection, but we find little evidence of a host genetic basis for these effects. Across host species, we find no evidence of systematic changes in susceptibility during coinfection, with no interaction between DCV and CrPV detected in the majority of host species. These results suggest that phenotypic variation in coinfection interactions within host species can occur independently of natural host genetic variation in susceptibility, and that patterns of susceptibility across host species to single infections can be robust to the added complexity of coinfection.
Autorepression-based conditional gene expression system in yeast for variation-suppressed control of protein dosage
Authors: Azizoğlu Aslı , Loureiro Cristina , Venetz Jonathan , Brent Roger 
Published: December 2022

Conditional control of gene expression allows an experimenter to investigate many aspects of a gene’s function. In the model organismSaccharomyces cerevisiae, a number of methods to control gene expression are widely practiced, including induction by metabolites, small molecules, and even light. However, all current methods suffer from at least one of a set of drawbacks, including need for specialized growth conditions, leaky expression, or the requirement of specialized equipment. Here we describe protocols using two transformations to construct strains that carry a new controller, in which all these drawbacks are overcome. In these strains, the expression of a controlled gene (gene of interest, or GOI) is repressed by the bacterial repressor TetR, and induced by anhydrotetracycline. TetR also regulates its own expression, creating an autorepression loop. This autorepression allows tight control of gene expression/ protein dosage with low cell to cell variation in expression. A second repressor, TetR-Tup1, prevents any leaky expression. We also present a protocol showing a particular workhorse application of such strains, to generate synchronized cell populations. We turn off the expression of the cell cycle regulatorCDC20completely, arresting the cell population, and then back on so that the synchronized cells resume cell cycle progression. This control system can be applied to any endogenous or exogenous gene for precise expression.Basic Protocol 1Generating a parent WTC846strain.Basic Protocol 2Generating a WTC846strain with controlled expression of the targeted geneAlternate Protocol 1CRISPR-mediated promoter replacementBasic Protocol 3Cell cycle synchronization/Arrest and Release using the WTC846-K3::CDC20 strain
Uncovering the genomic basis of infection through co-genomic sequencing of hosts and parasites
Authors: Dexter Eric , Fields Peter D. , Ebert Dieter 
Published: December 2022

AbstractUnderstanding the genomic basis of infectious disease is fundamental objective in coevolutionary theory with relevance to healthcare, agriculture, and epidemiology. Models of host-parasite coevolution often assume that infection requires specific combinations of host and parasite genotypes. Coevolving host and parasite loci are therefor expected to show associations that reflects an underlying infection/resistance allele matrix, yet little evidence for such genome-to-genome interactions has been observed among natural populations. We conducted a study to search for this genomic signature across 258 linked host (Daphnia magna)and parasite (Pasteuria ramosa)genomes. Our results show a clear signal of genomic association between multiple epistatically-interacting loci in the host genome, and a family of genes encoding for collagen-like protein in the parasite genome. These findings are supported by laboratory-based infection trials, which show strong correspondence between phenotype and genotype at the identified loci. Our study provides clear genomic evidence of antagonistic coevolution among wild populations.
★Track: Inferred counting and tracking of replicating DNA loci
Authors: Köhler Robin , Sadhir Ismath , Murray Seán M. 
Published: December 2022

AbstractFluorescent microscopy is the primary method to study DNA organization within cells. However the variability and low signal-to-noise commonly associated with live-cell time lapse imaging challenges quantitative measurements. In particular, obtaining quantitative or mechanistic insight often depends on the accurate tracking of fluorescent particles. Here, we present★Track, an inference method that determines the most likely temporal tracking of replicating intracellular particles such DNA loci while accounting for missing, merged and spurious detections. It allows the accurate prediction of particle copy numbers as well as the timing of replication events. We demonstrate★Track’s abilities and gain new insight into plasmid copy number control and the volume dependence of bacterial chromosome replication initiation. By enabling the accurate tracking of DNA loci,★Track can help to uncover the mechanistic principles of chromosome organisation and dynamics across a range of systems.SignificanceMicroscopy is one of the main tools for studying the intracellular organisation of cells. In particular, fluorescent proteins allow us to study the dynamics of many cellular processes. However, this requires the accurate tracking of fluorescent foci. Here, we present★Track a tool tailored to the tracking of replicating persistent subcellular particles such as DNA loci.★Track provides accurate predictions of particle copy number and replication timing even in the presence of substantial noise. The knowledge of these quantities are critical for uncovering the mechanisms behind many cell-cycle dependent processes, such the control of chromosome and plasmid replication initiation.
The build-up of the present-day tropical diversity of tetrapods
Authors: Quintero Ignacio , Landis Michael , Jetz Walter , Morlon Hélène 
Published: December 2022

AbstractThe extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatio-temporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.
Validation of Fuze IMU system for ergonomics assessments
Authors: Serra-Hsu Elizabeth , Taboga Paolo 
Published: December 2022

AbstractThis study aims to validate the Fuze system (SwiftMotion, CA, USA), against the gold standard for motion capture, a 3D infra-red motion capture system (Vicon Nexus, Oxford, UK). Fuze system uses inertial measurement units and proprietary algorithms to calculate position and orientation of each body segmentSix subjects (3M and 3F) performed two activities that simulate common occupational physical activities. For both systems, we calculated the following joint angles: trunk relative to horizontal, left and right shoulder and hip joint angles. We also calculated the horizontal distance of each wrist relative to the the fifth lumbar vertebra. For each measurement, we calculated Bias (average difference between Fuze and Vicon system) and root mean squared error (RMSE). We also compared each measurement using a Statistical Parametric Mapping (SPM) method with a statistical significance level set at 0.05.Compared to Vicon, Fuze system had a maximum Bias of 5.63 ± 1.60 degrees for the left shoulder angle and a maximum RMSE of 10.03 ± 2.73 degrees for the left hip angle. SPM analysis evidenced that for all the measurements, comparisons were within the critical thresholds for significance for the whole duration of the trials, indicating that we could not find a significant difference between Vicon and Fuze measurements.In conclusion: the Fuze system compares well with the Vicon system and provides reliable data for the measurement of joint angles and body positions, that can be used in particular in non labbased settings, for example in ergonomics risk assessments.
Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
Authors: Chen Xi , Wang Yuan , Cappuccio Antonio , Cheng Wan-Sze , Zamojski Frederique Ruf , Nair Venugopalan D. , Miller Clare M. , Rubenstein Aliza B. , Nudelman German , Tadych Alicja , Theesfeld Chandra L. , Vornholt Alexandria , George Mary-Catherine , Ruffin Felicia , Dagher Michael , Chawla Daniel G. , Soares-Schanoski Alessandra , Spurbeck Rachel R. , Ndhlovu Lishomwa C. , Sebra Robert , Kleinstein Steven H. , Letizia Andrew G. , Ramos Irene , Fowler Vance G. , Woods Christopher W. , Zaslavsky Elena , Troyanskaya Olga G. , Sealfon Stuart C. 
Published: December 2022

AbstractResolving chromatin remodeling-linked gene expression changes at cell type resolution is important for understanding disease states. We describe MAGICAL, a hierarchical Bayesian approach that leverages paired scRNA-seq and scATAC-seq data from different conditions to map disease-associated transcription factors, chromatin sites, and genes as regulatory circuits. By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference. We applied MAGICAL to studyStaphylococcus aureussepsis from peripheral blood mononuclear single-cell data that we generated from infected subjects with bloodstream infection and from uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be activated by bacterial sepsis. We addressed the challenging problem of distinguishing host regulatory circuit responses to methicillin-resistant-(MRSA) and methicillin-susceptibleStaphylococcus aureus(MSSA) infections. While differential expression analysis failed to show predictive value, MAGICAL identified epigenetic circuit biomarkers that distinguished MRSA from MSSA.