bluuebunny/crossref_metadata_2025_split huggingface dataset:
StrainDesign: a comprehensive Python package for computational design of metabolic networks
Authors: Schneider Philipp , Bekiaris Pavlos Stephanos , von Kamp Axel , Klamt Steffen 
Published: September 2022

Abstract

Summary
Various constraint-based optimization approaches have been developed for the computational analysis and design of metabolic networks. Herein, we present StrainDesign, a comprehensive Python package that builds upon the COBRApy toolbox and integrates the most popular metabolic design algorithms, including nested strain optimization methods such as OptKnock, RobustKnock and OptCouple as well as the more general minimal cut sets approach. The optimization approaches are embedded in individual modules, which can also be combined for setting up more elaborate strain design problems. Advanced features, such as the efficient integration of GPR rules and the possibility to consider gene and reaction additions or regulatory interventions, have been generalized and are available for all modules. The package uses state-of-the-art preprocessing methods, supports multiple solvers and provides a number of enhanced tools for analyzing computed intervention strategies including 2D and 3D plots of user-selected metabolic fluxes or yields. Furthermore, a user-friendly interface for the StrainDesign package has been implemented in the GUI-based metabolic modeling software CNApy. StrainDesign provides thus a unique and rich framework for computational strain design in Python, uniting many algorithmic developments in the field and allowing modular extension in the future.

Availability and implementation
The StrainDesign package can be retrieved from PyPi, Anaconda and GitHub (https://github.com/klamt-lab/straindesign) and is also part of the latest CNApy package.
Practicing Lived Experience Leadership with Love: Photovoice Reflections of a Community-Led Crime Prevention Project
Authors: Buck Gillian , Ryan Kemi , Ryan Natasha 
Published: September 2022

AbstractLived experience leadership is part of a broader international trend towards service user involvement in public services yet little is known about services developed and delivered by people with lived experience of the criminal justice system. Our innovative study, coproduced by two formerly imprisoned community practitioners and an academic researcher, aims to amplify the voices of people delivering and using a lived experience-led crime prevention project. Using photovoice methods, in which people use cameras to document their realities and advocate for change, we explore the potential of lived experience leadership to drive individual and social change. Some of the compelling images produced by the group are showcased, revealing how in contexts of suffering, social exclusion and negative expectations, forms of inclusive, loving, hopeful community praxis can be impactful. We conclude that allegiances between community practitioners and social workers could begin to disrupt harmful and oppressive structures and create locally led, hope-filled service provision. To broker such allied practices, we include a self-audit for social and community workers, inviting reflections focused on this ambitious goal.
Impact of segmentectomy and lobectomy on non-lung cancer death in early-stage lung cancer patients
Authors: Isaka Tetsuya , Ito Hiroyuki , Yokose Tomoyuki , Saito Haruhiro , Adachi Hiroyuki , Miura Jun , Murakami Kotaro , Rino Yasushi 
Published: September 2022

Abstract

OBJECTIVES
This study aimed to analyse the risk of death from non-lung cancer after segmentectomy or lobectomy for early-stage lung cancer.

METHODS
A total of 1385 patients underwent lobectomy or segmentectomy for clinical stage 0–I primary lung cancer, with no evidence of recurrence after surgery, between January 2008 and December 2018. Risk factors for non-lung cancer deaths (NLCD) were analysed using multivariable logistic regression analysis. The overall survival (OS) of patients with low and high comorbidities who underwent lobectomy and segmentectomy was compared using a log-rank test.

RESULTS
Patients with NLCD (n = 126) were more likely to have undergone lobectomy than patients with non-recurrence survival (n = 1259). Multivariable analysis revealed that age (≥65 years), smoking index (≥600), body mass index (≤18.5 kg/m2), interstitial pneumonia, values for percentage of predicted vital capacity (≤9.4%) and lobectomy were risk factors for NLCD. Patients who underwent segmentectomy had significantly better 5-year OS than those who underwent lobectomy, after propensity score matching (94.6% vs 90.4%, P = 0.027). Patients with high comorbidities (patients with ≥2 of the following risks: age ≥65 years, smoking index ≥600, body mass index ≤18.5 kg/m2, Charlson Comorbidity Index ≥1, values for percentage of predicted vital capacity ≤96.4%) who underwent segmentectomy had a better 5-year OS than those who underwent lobectomy (92.8% vs 87.8%, P = 0.016). However, there was no difference in 5-year OS between segmentectomy and lobectomy in patients with low comorbidities (98.5% vs 97.4%, P = 0.867).

CONCLUSIONS
The impact of lobectomy and segmentectomy on NLCD depends on the extent of the patients’ comorbidities.
Regimen of Coronavirus Disease 2019 Vaccination Influences Extent and Kinetics of Antibody Avidity
Authors: Rössler Annika , Kimpel Janine , Fleischer Verena , Huber Silke , von Laer Dorothee , Borena Wegene , Würzner Reinhard ,   the HEVACC Study Group, Bante David , Falkensammer Barbara , Schäfer Helena , Krammer Florian , Pichler Peter , Wiedermann Ursula , Rainer Daniel , Trips Tobias , Zabernigg August 
Published: September 2022

Abstract
We investigated antibody titers and avidity after heterologous versus homologous coronavirus disease 2019 vaccination over 6 months after the second dose. We found a significantly higher avidity in regimens including at least 1 dose of the adenoviral vector vaccine ChAdOx1-S compared with 2 doses of the mRNA vaccine BNT162b2.
Abdominal Movements in Insect Flight Reshape the Role of Non-Aerodynamic Structures for Flight Maneuverability I: Model Predictive Control for Flower Tracking
Authors: Bustamante Jorge , Ahmed Mahad , Deora Tanvi , Fabien Brian , Daniel Thomas L 
Published: September 2022

Synopsis
Research on insect flight control has focused primarily on the role of wings. Yet abdominal deflections during flight can potentially influence the dynamics of flight. This paper assesses the role of airframe deformations in flight, and asks to what extent the abdomen contributes to flight maneuverability. To address this, we use a combination of both a Model Predictive Control (MPC)-inspired computational inertial dynamics model, and free flight experiments in the hawkmoth, Manduca sexta. We explored both underactuated (i.e., number of outputs are greater than the number of inputs) and fully actuated (equal number of outputs and inputs) systems. Using metrics such as the non-dimensionalized tracking error and cost of transport to evaluate flight performance of the inertial dynamics model, we show that fully actuated simulations minimized the tracking error and cost of transport. Additionally, we tested the effect of restricted abdomen movement on free flight in live hawkmoths by fixing a carbon fiber rod over the thoracic-abdomen joint. Moths with a restricted abdomen performed worse than sham treatment moths. This study finds that abdominal motions contribute to flight control and maneuverability. Such motions of non-aerodynamic structures, found in all flying taxa, can inform the development of multi-actuated micro air vehicles.
On the Aesthetic Appreciation of Damaged Environments
Authors: Alcaraz León María José 
Published: September 2022

Abstract
As aesthetic appreciators of the environment, we often encounter cases where our environmental commitments and our aesthetic responses do not seem to match. Some highly altered or contaminated environments may occasion powerful and insightful aesthetic experiences. In this article, I discuss some arguments that have been offered in favor of the view that this mismatch is not possible when we appreciate a particular environment with full awareness of its damaged or altered condition. I show that these arguments are not conclusive and that there is room for valuable experiences of damaged or highly altered environments. Our knowledge of the damaged condition of an environment, while perceptually significant, does not necessarily make the resulting aesthetic experience to be negative. Finally, I show that these cases do not necessarily diminish the role that aesthetics can play in shaping our environmental sensibility and commitments.
Status of Onchocerca volvulus (Spirurida: Onchocercidae) Transmission and Effect of Climatic Variables on the Vector Population Dynamics After Two Decades of Ivermectin-based Preventive Chemotherapy in the Mbam Valley (Centre Region, Cameroon)
Authors: Domche André , Nwane Philippe B , Nana Djeunga Hugues C , Njitchouang Guy R , Pion Sébastien D , Boussinesq Michel , Njiokou Flobert , Kamgno Joseph 
Published: September 2022

Abstract
Entomological indicators of onchocerciasis transmission and the effect of climatic variables on the vector population dynamics were investigated in two first-line villages after more than two decades of mass drug administration with ivermectin. Female blackflies were collected in two villages (Bayomen and Biatsota) using human landing method for a period of 12 months. Blackflies were dissected and entomological indices were computed. Monthly temperature, precipitation, and humidity were collected and the Spearman correlation rank test was used to assess the relationship between biting rates and climatic variables. The highest biting rates (62,280 bites/human/month in Bayomen and 42,090 bites/human/month in Biatsota) were recorded during the long rainy season (November). The Onchocerca volvulus transmission was greater during the long dry season in both villages, with a peak at the beginning of the long dry season in Biatsota (100 infective larvae/human/month), and at the middle of the long dry season in Bayomen (92 infective larvae/human/month). No correlation was found between biting rates and selected climatic variables in the two villages. This study revealed that onchocerciasis transmission is ongoing in the study area despite almost 25 years of Community-Directed Treatment with Ivermectin. In accordance with WHO recommendations, vector control should be used in combination with mass drug administration to accelerate transmission interruption of onchocerciasis. To be optimal, this vector control should be implemented during the long dry season (November to March) when water volumes are low and transmission potentials are high.
PNV J00444033+4113068: Early superhumps with 0.7 mag amplitude and non-red color
Authors: Tampo Yusuke , Isogai Keisuke , Kojiguchi Naoto , Uemura Makoto , Kato Taichi , Tordai Tamás , Vanmunster Tonny , Itoh Hiroshi , Dubovsky Pavol A , Medulka Tomáš , Sano Yasuo , Hambsch Franz-Josef , Taguchi Kenta , Maehara Hiroyuki , Ito Junpei , Nogami Daisaku 
Published: September 2022

Abstract
In the first days of WZ Sge-type dwarf nova (DN) outbursts, the 2 : 1 resonance induces a spiral arm structure in the accretion disk, which is observed as early superhumps in optical light curves. We reports on our optical observations of an eclipsing WZ Sge-type DN PNV J00444033+4113068 during its 2021 superoutburst using the 3.8 m Seimei telescope and through the Variable Star Network collaboration. The eclipse analysis showed that its orbital period was 0.055425534(1) d. Our observations confirmed early superhumps with an amplitude of 0.7 mag, the largest amplitude among known WZ Sge-type DNe. More interestingly, its early superhumps became the reddest around their secondary minimum, whereas other WZ Sge-type DNe show the reddest color around the early superhump maximum. The spectrum around the peak of the outburst showed two double-peaked emission lines of He ii 4686 Å and Hα with a peak separation of ≥700 km s−1, supporting a very high-inclination system. With the early superhump mapping, the unique profile and color of the early superhump are successfully reproduced by an accretion disk with a vertically extended double arm structure. Therefore, a large amplitude and a unique color behavior of the early superhumps in PNV J00444033+4113068 can be explained by the 2 : 1 resonance model along with other WZ Sge-type DNe.
Down-regulated FcγRII expression on plasma cells is associated with the disease activity of ANCA-associated vasculitis
Authors: Wang Chen , Gong Yan , You Ran , Li Zhi-Ying , Zhao Ming-Hui , Chen Min 
Published: September 2022

Abstract

Objectives
Inhibitory FcγRIIB/CD32B on B cells are critical for immunity regulation to help maintain peripheral tolerance. Altered FcγRIIB expression on B cells has been observed in several autoimmune diseases, and animal studies have suggested that FcγRIIB on B cells participates in the pathogenesis of ANCA-associated vasculitis (AAV). Here, we investigated the expression of FcγRII (FcγRIIB) on various B cell subsets and the correlation of FcγRII/CD32 expression with disease activity in AAV patients.

Material and methods
Blood samples of patients with AAV in active stage and in remission were collected. FcγRII/CD32 expressions on various B cell subsets of the whole blood were detected by flow cytometry, and their correlation with clinical and pathological data was analysed.

Results
The expression of FcγRII/CD32 on plasma cells was significantly lower in AAV patients in active stage than those in both AAV patients in remission and healthy donors. Furthermore, the expression of FcγRII/CD32 on plasma cells negatively correlated with BVAS and percentages of cellular crescents in renal biopsies.

Conclusions
There is a down-regulation of FcγRIIB/CD32B expression on B cells in patients with AAV, which is associated with the disease activity of AAV.
Host prediction for disease-associated gastrointestinal cressdnaviruses
Authors: Kinsella Cormac M , Deijs Martin , Becker Christin , Broekhuizen Patricia , van Gool Tom , Bart Aldert , Schaefer Arne S , van der Hoek Lia 
Published: September 2022

Abstract
Metagenomic techniques have facilitated the discovery of thousands of viruses, yet because samples are often highly biodiverse, fundamental data on the specific cellular hosts are usually missing. Numerous gastrointestinal viruses linked to human or animal diseases are affected by this, preventing research into their medical or veterinary importance. Here, we developed a computational workflow for the prediction of viral hosts from complex metagenomic datasets. We applied it to seven lineages of gastrointestinal cressdnaviruses using 1,124 metagenomic datasets, predicting hosts of four lineages. The Redondoviridae, strongly associated to human gum disease (periodontitis), were predicted to infect Entamoeba gingivalis, an oral pathogen itself involved in periodontitis. The Kirkoviridae, originally linked to fatal equine disease, were predicted to infect a variety of parabasalid protists, including Dientamoeba fragilis in humans. Two viral lineages observed in human diarrhoeal disease (CRESSV1 and CRESSV19, i.e. pecoviruses and hudisaviruses) were predicted to infect Blastocystis spp. and Endolimax nana respectively, protists responsible for millions of annual human infections. Our prediction approach is adaptable to any virus lineage and requires neither training datasets nor host genome assemblies. Two host predictions (for the Kirkoviridae and CRESSV1 lineages) could be independently confirmed as virus–host relationships using endogenous viral elements identified inside host genomes, while a further prediction (for the Redondoviridae) was strongly supported as a virus–host relationship using a case–control screening experiment of human oral plaques.
Anxiety in heart failure patients and its association with socio-demographic and clinical characteristics: a cross-sectional study
Authors: Costa Filipa M. D. , Martins Sónia P. V. , Moreira Emilia C. T. D. , Cardoso José C. M. S. , Fernandes Lia P. N. S. 
Published: September 2022

Background:
Anxiety is one of the most frequent psychiatric disorders in heart failure (HF) patients. However, it is often neglected in clinical practice and studies about the particular relationship with the New York Heart Association (NYHA) classes for HF are scarce. In this context, this study aims to analyze the presence of anxiety symptoms in HF outpatients and also its association with sociodemographic and clinical characteristics of these patients.

Methods:
This cross-sectional study is part of the longitudinal Deus Ex-Machina project (NORTE-01-0145-FEDER-000026). HF patients were recruited at an outpatient clinic at a University Hospital. Patients with inability to communicate, severe visual/hearing impairment, or NYHA class IV were excluded. Sociodemographic data and NYHA class were registered. Anxiety was assessed with the 7-item Generalized Anxiety Disorders Scale (with a score ≥10 clinically relevant anxiety). Patients with and without anxiety were compared regarding socio-demographic and clinical variables.

Results:
The sample (n = 136) had a median age of 59years (Q1: 49; Q3: 68), 66.2% were male and 31.6% presented clinically relevant anxiety. A higher percentage of HF patients with anxiety had psychiatric disorders (58.1% vs 26.9%; P = .001), psychotropic medication (62.8% vs 30.1%; P = .001), and depression (60.5% vs 9.7%; P< .001). No significant differences were found regarding the remaining variables, including NYHA classes.

Conclusions:
A substantial proportion of HF patients present clinically relevant anxiety, particularly those with psychiatric history, depressive symptoms, or under psychotropic medication. Therefore, integrating routine screening and treatment of this comorbidity in clinical practice is of utmost importance. Further studies are needed to clarify the association of anxiety with HF.
Acuity Tools for the Antepartum and Neonatal Intensive Care Units
Authors: Roth Cheryl , Dent Sarah A. , Luster Mary H. , Hering Sandra L. , Bay R. Curtis 
Published: September 2022

Abstract

Purpose:
To evaluate content validity and interrater reliability for acuity tools developed for the antepartum and neonatal intensive care unit (NICU) patient population.

Study Design and Methods:
Antepartum and NICU acuity tools were developed to better evaluate nurse staffing assignment equity and patient needs. Following several iterations with staff nurses and nurse leaders, content validity of the acuity tools was established via a panel of experts in each substantive area using the Content Validity Index. The final tools were then evaluated for interrater reliability using Intraclass Correlation.

Results:
Content validity for the Antepartum Acuity Tool was S-CVI/Ave = 0.87 and for the NICU Acuity Tool was S-CVI/Ave = 0.98. Interrater Reliability for the Antepartum Acuity tool was ICC = 0.88, and the NICU Acuity Tool was ICC = 0.95.

Clinical Implications:
These tools have established content validity and interrater reliability and are appropriate for use in the antepartum and NICU settings to determine patient acuity and promote appropriate nurse-to-patient assignments.
Transgender and Nonbinary Deaths Investigated by the State Medical Examiner in the Portland, Oregon, Metro Area and Their Concordance With Vital Records, 2011-2021
Authors: Walters Jaime K. , Mew Molly C. , Repp Kimberly K. 
Published: September 2022

Objectives:
To illustrate possible improvements in recording of gender identity, we investigated discrepancies between gender identity from medical examiner (ME) death investigations and sex as recorded in the final death record.

Design:
Evaluation of a database used to record information related to medicolegal death investigation with matching to state vital records. Kappa analysis was used to measure concordance between both systems.

Setting:
The Portland, Oregon, metro area (Clackamas, Multnomah, and Washington Counties) and deaths investigated by the Offices of each County Medical Examiner between January 2011 and September 2020.

Intervention:
Epidemiologists identified incongruous data that have significant negative implications for transgender populations. Epidemiologists identified key actions that, if taken by death investigators, death record software, and the federal death certificate form, will rectify harmful data discrepancies.

Main Outcome Measure:
Concordance of gender identity and sex in ME data and death record, respectively.

Results:
We identified 51 deaths in transgender persons; the majority were classified as transgender female (71%). The κ statistic was −0.0657, indicating poor concordance between the gender identity in ME investigation and the death certificate in vital records.

Conclusions:
Information gathered via medicolegal death investigations is foundational to effective public health/public safety response; MEs and coroners are often the first to document emerging health threats. Discrepancies in official death records impede accurate surveillance of a population disproportionately at risk of violent death.
The global burden of cognitive impairment in people with HIV
Authors: Keng Lea D. , Winston Alan , Sabin Caroline A. 
Published: September 2022

Objective:
While life expectancies of people with HIV (PWH) have increased through the successes of antiretroviral treatment, cognitive impairment remains a pressing concern. Prevalence estimates vary worldwide as different definitions for cognitive impairment are used and resource availability differs across geographical settings. We aim to explore this heterogeneity and estimate the global cognitive impairment burden in PWH.

Design:
Systematic literature review and meta-analysis.

Methods:
We searched PubMed, Embase, SCOPUS, and Web of Science for studies reporting on cognitive impairment prevalence in PWH. Nine factors were investigated for their potential association with the prevalence using a univariate meta-analysis and a meta-regression: assessment method, geographical region, country income, exclusion criteria, study quality, age, sex, publication year, and sample size.

Results:
The literature search identified 8539 records, of which 225 were included. The adjusted prevalence was significantly lower in males than females. Across 44 countries, 12 assessment methods were used; the HIV-associated neurocognitive disorder/Frascati criteria, known for high false-positive rates, was employed in 44.4% of studies. The pooled cognitive impairment prevalence estimate in PWH, including asymptomatic cases, was 39.6% (95% confidence interval: 37.2–42.1%; range: 7–87%). The meta-regression explained 13.3% of between-study variation, with substantial residual heterogeneity (I
2 = 97.7%).

Conclusion:
Lack of data from more than 70% of the world's countries, cohorts being unselected for symptoms in most research studies, and limitations of the HIV-associated neurocognitive disorder/Frascati criteria restrict the ability to accurately determine the global burden of cognitive impairment in PWH. More studies in low-resource settings and a standardized approach to assessing cognitive impairment, bridging research and clinical realms, are needed.