bluuebunny/crossref_metadata_2025_split huggingface dataset:
TOSCCA: a framework for interpretation and testing of sparse canonical correlations
Authors: Senar Nuria , van de Wiel Mark , Zwinderman Aeilko H , Hof Michel H 
Published: February 2024

Abstract

Summary
In clinical and biomedical research, multiple high-dimensional datasets are nowadays routinely collected from omics and imaging devices. Multivariate methods, such as Canonical Correlation Analysis (CCA), integrate two (or more) datasets to discover and understand underlying biological mechanisms. For an explorative method like CCA, interpretation is key. We present a sparse CCA method based on soft-thresholding that produces near-orthogonal components, allows for browsing over various sparsity levels, and permutation-based hypothesis testing. Our soft-thresholding approach avoids tuning of a penalty parameter. Such tuning is computationally burdensome and may render unintelligible results. In addition, unlike alternative approaches, our method is less dependent on the initialization. We examined the performance of our approach with simulations and illustrated its use on real cancer genomics data from drug sensitivity screens. Moreover, we compared its performance to Penalized Matrix Analysis (PMA), which is a popular alternative of sparse CCA with a focus on yielding interpretable results. Compared to PMA, our method offers improved interpretability of the results, while not compromising, or even improving, signal discovery.

Availability and implementation
The software and simulation framework are available at https://github.com/nuria-sv/toscca.
SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space
Authors: Biyuzan Hamza , Masrour Mohamed-Akram , Grandmougin Lucas , Payan Frédéric , Douguet Dominique 
Published: February 2024

Abstract

Motivation
Popular shape-based alignment methods handle molecular flexibility by utilizing conformational ensembles to select the most fitted conformer. However, the initial conformer library generation step is computationally intensive and limiting to the overall alignment process. In this work, we describe a method to perform flexible alignment of two molecular shapes by optimizing the 3D conformation. SENSAAS-Flex, an add-on to the SENSAAS tool, is able to proceed from a limited set of initial conformers through an iterative process where additional conformational optimizations are made at the substructure level and constrained by the target shape.

Results
In self- and cross-alignment experiments, SENSAAS-Flex is able to reproduce the crystal structure geometry of ligands of the AstraZeneca Molecule Overlay Test set and PDBbind refined dataset. Our study shows that the point-based representation of molecular surfaces is appropriate in terms of shape constraint to sample the conformational space and perform flexible molecular alignments.

Availability and implementation
The documentation and source code are available at https://chemoinfo.ipmc.cnrs.fr/Sensaas-flex/sensaas-flex-main.tar.gz
Effectiveness of Partial Enteral Nutrition as Add-On to Biologics in Patients With Refractory and Difficult-to-Treat Crohn’s Disease: A Pilot Study
Authors: Nardone Olga Maria , Calabrese Giulio , La Mantia Alessia , Testa Anna , Rispo Antonio , Alfonsi Lucia , Pasanisi Fabrizio , Castiglione Fabiana 
Published: February 2024

Abstract

Background
Partial enteral nutrition (PEN) is a well-established treatment for children with Crohn’s disease (CD). However, its efficacy in adults with CD remains uncertain. We aimed to assess the effectiveness of PEN as an add-on to escalated biological therapy in adults with CD who have lost response to biologics.

Methods
We conducted a retrospective observational study including patients who had lost response to biologics and received PEN in combination with escalated treatment, compared to those treated only with escalated therapy. The primary endpoint was steroid-free clinical remission (CR) at 24 weeks. Secondary endpoints included transmural healing (TH) and response (TR) rates along with selected clinical outcomes.

Results
Forty-two patients were screened; 12 (28.6%) were excluded for complicated disease and 30 (71.4%) were included in the final analysis. Fourteen (46.7%) patients completed PEN treatment at 8 weeks, while 16 patients (53.3%) discontinued treatment due to intolerance and continued with escalation of biologic (BT group). At 24 weeks, 9 patients (64.3%) in the PEN group achieved CR, compared to 4 patients (25%) in the BT group (P = .03). The TR rate was 64.9% in the PEN group and 25% in the BT group (P = .03). Patients receiving PEN exhibited an increase in albumin levels compared to those in the BT group (Δ = 0.5; P = .02). A higher rate of therapy changes (68.7%) was observed in the BT group compared to 14.2% in the PEN group (P = .004). Prior failure to 2 lines of biological therapy was associated with adherence to PEN (OR = 1.583; CI = 1.06-2.36; P = .01).

Conclusions
In patients who had lost response to biologics, PEN in combination with escalated biologics was associated with CR and TR and improved nutritional status. Hence, the addition of PEN should be considered for patients with difficult-to-treat CD.
Genetic architecture of trait variance in craniofacial morphology
Authors: Andrade Fernando , Howell Lisa , Percival Christopher J , Richtsmeier Joan T , Marcucio Ralph S , Hallgrímsson Benedikt , Cheverud James M 
Published: February 2024

Abstract
The genetic architecture of trait variance has long been of interest in genetics and evolution. One of the earliest attempts to understand this architecture was presented in Lerner's Genetic Homeostasis (1954). Lerner proposed that heterozygotes should be better able to tolerate environmental perturbations because of functional differences between the alleles at a given locus, with each allele optimal for slightly different environments. This greater robustness to environmental variance, he argued, would result in smaller trait variance for heterozygotes. The evidence for Lerner's hypothesis has been inconclusive. To address this question using modern genomic methods, we mapped loci associated with differences in trait variance (vQTL) on 1,101 individuals from the F34 of an advanced intercross between LG/J and SM/J mice. We also mapped epistatic interactions for these vQTL in order to understand the influence of epistasis for the architecture of trait variance. We did not find evidence supporting Lerner's hypothesis, that heterozygotes tend to have smaller trait variances than homozygotes. We further show that the effects of most mapped loci on trait variance are produced by epistasis affecting trait means and that those epistatic effects account for about a half of the differences in genotypic-specific trait variances. Finally, we propose a model where the different interactions between the additive and dominance effects of the vQTL and their epistatic partners can explain Lerner's original observations but can also be extended to include other conditions where heterozygotes are not the least variable genotype.
Predictors of Frailty Transitions in Mexican Older Adults
Authors: Rivera-Almaraz Ana , Salinas-Rodríguez Aarón , Gutiérrez-Peña Eduardo , Manrique-Espinoza Betty Soledad 
Published: February 2024

Abstract

Background
Frailty is a dynamic state in older adults. Current evidence, mostly in high-income countries, found that improving frailty is more likely in mild states (prefrailty). We aimed to determine the probability of frailty transitions and their predictors.

Methods
Participants were adults aged 50 years or over from the Study on Global Ageing and Adult Health in Mexico during 4 waves (2009, 2014, 2017, and 2021). We defined frailty with the frailty phenotype and we used multinomial logistic models to estimate the probabilities of frailty transitions and determine their predictors.

Results
For the 3 analyzed periods (2009–2014, 2014–2017, and 2017–2021), transition probabilities from frail to robust were higher for the younger age group (50–59 years) at 0.20, 0.26, and 0.20, and lower for the older age group (≥80 years), 0.03, 0.08 and 0.04. Transitioning from prefrail to robust had probabilities of 0.38, 0.37, and 0.35, for the younger age group, and 0.09, 0.18, and 0.10, for the older age group. The probabilities of transitioning to frail and to death were lower for the younger age group and for the robust at baseline; but higher for the older age group and for the frail at baseline. We identified age, disability, and diabetes as the most significant predictors of frailty transitions.

Conclusions
These findings show that frailty has a dynamic nature and that a significant proportion of prefrail and frail individuals can recover to a robust or prefrail state. They also emphasize that prefrailty should be the focus of interventions.
Hospital prescribing patterns of antibiotics in Zambia using the WHO prescribing indicators post-COVID-19 pandemic: findings and implications
Authors: Mudenda Steward , Chilimboyi Robert , Matafwali Scott Kaba , Daka Victor , Mfune Ruth Lindizyani , Kemgne Loriane Arielle Mobou , Bumbangi Flavien Nsoni , Hangoma Jimmy , Chabalenge Billy , Mweetwa Larry , Godman Brian 
Published: February 2024

AbstractBackgroundAntimicrobial resistance (AMR) is a global public health problem that is fuelled by the inappropriate prescribing of antibiotics, especially those from the ‘watch’ and ‘reserve’ antibiotic lists. The irrational prescribing of antibiotics is particularly prevalent in developing countries, including Zambia. Consequently, there is a need to better understand prescribing patterns across sectors in Zambia as a basis for future interventions. This study evaluated the prescribing patterns of antibiotics using the WHO prescribing indicators alongside the ‘access, watch and reserve’ (AWaRe) classification system post-COVID pandemic at a faith-based hospital in Zambia.MethodsA cross-sectional study was conducted from August 2023 to October 2023 involving the review of medical records at St. Francis’ Mission Hospital in Zambia. A WHO-validated tool was used to evaluate antibiotic prescribing patterns alongside the AWaRe classification tool.ResultsOut of 800 medical records reviewed, 2003 medicines were prescribed. Each patient received an average of 2.5 medicines per prescription. Antibiotics were prescribed in 72.3% of encounters, of which 28.4% were injectable. The most frequently prescribed antibiotics were amoxicillin (23.4%—access), metronidazole (17.1%—access), ciprofloxacin (8%—watch) and ceftriaxone (7.4%—watch), with 77.1% overall from the ‘access’ list. Encouragingly, 96.5% of the medicines were prescribed by their generic names and 98% were from the Zambia Essential Medicines List.ConclusionsThere were high rates of antibiotic prescribing, including injectable antibiotics, which needs addressing going forward. It is crucial to implement targeted measures, including antimicrobial stewardship programmes, to improve future antibiotic prescribing in Zambia and reduce the risk of AMR.
Nucleocapsid and Spike Protein-Based Anti-SARS-CoV-2 Assay Performance in the Minority and Rural Coronavirus Insights Study: Characteristics of Socioeconomically Disadvantaged Populations with Health Disparities
Authors: Christenson Robert H , Hansel Shantoy , II'yasova Dora , Meyer William A , Puckrein Gary , Lee LaTasha , Landry Latrice G , Akinboboye Ola 
Published: February 2024

Abstract

Background
COVID-19 has had a devastating impact on Black, Hispanic, and other underserved, disadvantaged populations. Here anti-SARS-CoV-2 tests are characterized in disadvantaged patients to examine equivalence in US populations.

Methods
Underserved participant adults (age &gt; 18 years) were enrolled before the availability of SARS-CoV-2 vaccines in Federal Qualified Health Centers in California, Florida, Louisiana, Illinois, and Ohio and contributed samples to the Minority and Rural Coronavirus Insights Study (MRCIS). A subset coined the MRCIS SARS-CoV-2 Antibody Cohort of 2365 participants was tested with the Roche Anti-SARS-CoV-2 assay (Cobas e601). Five hundred ninety-five of these were also tested with the Ortho Clinical Diagnostics VITROS Anti-SARS-CoV-2 IgG assay (VITROS-5600); 1770 were also tested with the Abbott ARCHITECT SARS-CoV-2 IgG assay (ARCHITECT-2000). Assay-specific cutoffs classified negative/positive results.

Results
Eight point four percent (199/2365) of the MRCIS SARS-CoV-2 Antibody Cohort was SARS-CoV-2 RNA positive at enrollment. Agreement between the Ortho/Roche and the Abbott/Roche antibody testing did not vary by enrollment RNA status. The Ortho (anti-spike protein) vs Roche (anti-nucleocapsid protein) comparison agreed substantially: kappa = 0.63 (95% CI: 0.57–0.69); overall agreement, 83%. However, agreement was even better for the Abbott vs Roche assays (both anti-nucleocapsid protein tests): kappa = 0.85 (95% CI: 0.81–0.87); overall agreement, 95%. Anti-SARS-CoV-2 comparisons stratified by demographic criteria demonstrated no significant variability in agreement by sex, race/ethnicity, or age.

Conclusions
Analytical agreement is 96.4% for anti-spike-protein vs anti-nucleocapsid-protein comparisons. Physiologically, seroreversion of anti-nucleocapsid reactivity after infection occurred in the disadvantaged population similarly to general populations. No anti-SARS-CoV-2 assays included demonstrated a clinically significant difference due to the demographics of the disadvantaged MRCIS SARS-CoV-2 Antibody Cohort.
Police militarization and local sheriff elections
Authors: Mavridis Christos , Troumpounis Orestis , Zanardi Maurizio 
Published: February 2024

Abstract
We investigate how transfers of military equipment in the United States through the 1033 Program impact the electoral performance of sheriffs that receive a significant share of equipment while directly accountable to voters. To address this question, we have compiled a unique dataset covering 7281 sheriff elections in 2714 counties between 2006 and 2016. Our findings indicate that an increase in military transfers to the sheriff’s office, from no transfers to the 25th percentile, increases the probability of the incumbent being reelected by 5.8–12.5 percentage points. This is due to an increase in the number of votes cast for the incumbent while there is no effect on the total number of voters participating in the election. Our heterogeneity results demonstrate that voters tend to reward military equipment transfers, especially when local newspapers are present and in Republican-leaning small counties, providing novel insights into voter responsiveness in local elections (JEL D72, H56, H76, K42).
Appendiceal duplication: a case report of horseshoe-shaped appendix and implications for patient safety
Authors: Deflaoui Tarik , Derkaoui Anas , Mahmoudi Mohammed , Akil Yassir , Amara Rihab , Miry Nadir , Amal Benani , Jabi Rachid , Bouziane Mohammed 
Published: February 2024

Abstract
Appendiceal anomalies, particularly double appendices, are rare and mainly detected during non-appendiceal surgery in adults. Misrecognizing them can have serious consequences, both clinically and legally. It is critical that surgeons pay attention to the anatomical variations of the vermiform appendix, and always consider the possibility of duplicated appendix when diagnosing a right iliac fossa pain. Misdiagnosis can lead to life-threatening medical complications for the patient, with medico-legal implications.
Biases in responding
Authors: Streiner David L. , Norman Geoffrey R. , Cairney John 
Published: February 2024

Abstract
Scale constructors hope that people will respond to the items by giving thoughtful and honest answers to every item. However, there are many biases that conspire against this, including end-aversion bias, social desirability bias, yea- and nay-saying, and others. The chapter discusses the different perspectives of the scale constructor and the respondent, and how this leads to some forms of bias. Answering questions is not as easy as we may imagine; there are many cognitive demands imposed by doing so, and these, too, can introduce other biases. The chapter also covers the effects of framing (how the question is worded), as well as the difficulties that are encountered in attempting to measure change. Finally, it discusses various ways of conducting cognitive interviews to ensure that the questions are being responded to as accurately as possible.
Clinical pharmacology
Authors: Currow David , Clark Katherine , Kleinig Paul 
Published: February 2024

Abstract
The interaction of medications with the person who has a life-limiting illness is critical to consider. Most people with a life-limiting illness have new medications introduced, while continuing their longer-term medications for their comorbid illnesses. Understanding the potential medication–person and medication–medication interactions is crucial to minimize harms and maximize benefits. In this setting, many people benefit from careful review of their medications to optimize their compliance with those medications that are most beneficial and, at the same time, to minimize harms.
Tricyclic Antidepressant Toxicity: Management of the Crashing Patient
Authors: Oram Matthew , Silva Joshua da 
Published: February 2024

Abstract
Although commonly used for treatment of depression in the 1950s, of tricyclic antidepressants (TCAs) have become less frequently prescribed with the widespread availability of selective serotonin reuptake inhibitors and serotonin and norepinephrine reuptake inhibitors (SNRIs). The TCA medication class carries with it a narrow therapeutic window and potential for lethal toxicity in overdose, and knowledge of its complications remains vital for any emergency physician. The primary therapeutic effect of TCAs comes via blockade of presynaptic norepinephrine and serotonin reuptake. Fatality in overdose most commonly occurs from cardiotoxicity mediated primarily via inhibition of fast sodium channels in the myocardium. Inhibition of myocardial potassium channels, hypotension from alpha-adrenergic blockade, and overexcitation of the CNS through gamma-aminobutyric acid (GABA) inhibition contribute to the class’s toxicity. Workup is focused on predicting overdose severity and evaluating for complicating factors such as co-ingestions and comorbidities. Treatment focuses on decreasing GI absorption in early overdose, prevention of arrhythmias, and treatment of hypotension. Knowledge of the pathophysiology, toxicity, and treatment of TCAs is vital information for ED physicians.
Diphenhydramine: The Cardiac Poison
Authors: Ugwu Chidiebere Victor , Hallett T. Christy 
Published: February 2024

Abstract
Diphenhydramine is an antihistamine with antimuscarinic properties commonly used to treat allergic reactions, acute dystonia, and insomnia. Overdose of this medication can be either intentional or due to misuse. Diphenhydramine absorption is quick due to its lipophilic nature, and it has a large volume of distribution. The clinical manifestation of this xenobiotic is multisystemic due to antimuscarinic effects and its sodium and potassium channel blockade. Diagnosis is made clinically in conjunction with a history of ingestion. Management of diphenhydramine overdose is primarily supportive, with the goal of monitoring and treating agitation, seizures, arrhythmias, hyperthermia, and rhabdomyolysis if they occur. Physostigmine is an anticholinergic antidote used to treat severe delirium or tachycardia but should be used cautiously due to possible adverse effects.
ME THink You Should Not Use: Methamphetamines Intoxication
Authors: Al-Sulaimani Suad 
Published: February 2024

Abstract
Methamphetamine is a highly addictive, commonly abused psychostimulant that is derived from phenethylamine. Methamphetamine abuse can result in acute and chronic serious health consequences, and use produces a hyper-adrenergic surge that ultimately leads to a variety of medical conditions. The acute effects of methamphetamines are caused by its sympathomimetic properties, and acute intoxication manifests with variable effects that range from agitation to hyperthermia, seizure, arrythmias, myocardial ischemia, and intracerebral hemorrhage and may lead to death. The choice of diagnostic workup depends on the clinical presentation. Qualitative urine immunoassays have limited utility in acutely intoxicated patients. Management of acute methamphetamine toxicity includes supportive care as well as treatment for acute agitation and psychosis. Benzodiazepines is the first-line treatment; repeated and escalated dosing is frequently required. Complications of adrenergic and serotonergic toxicity, such as hyperthermia and rhabdomyolysis, should be anticipated and managed aggressively.
Acetylcholine Overload: Organophosphate and Carbamate Exposures
Authors: Espinoza Luis , da Silva Joshua 
Published: February 2024

Abstract
Pesticides and insecticides containing organophosphates cause roughly 3 million poisonings and approximately 250,000 deaths worldwide every year. When exposed, these agents block acetylcholinesterase from breaking down acetylcholine, leading to a dangerous buildup of acetylcholine in the neuronal spaces. This accumulation continually stimulates postsynaptic nicotinic and muscarinic receptors, leading to a cholinergic toxidrome characterized by excess hyperstimulation of secretions and respiratory paralysis, as well as a host of other symptoms. If untreated, exposure can lead to coma and possibly death due to cardiorespiratory arrest and ventricular arrhythmias. In addition to a detailed history and thorough physical examination, patients require prompt decontamination and early treatment with atropine, titrated to dry respiratory secretions. Additional treatment may include pralidoxime (to prevent irreversible binding of organophosphates to acetylcholinesterase) and benzodiazepines (for treatment of seizures). Mortality of organophosphates can reach as high as 25%, making prompt recognition and early treatment vital for optimal chance of survival.
Occupational Health Services in policing: identifying the psychological burden to OHS team members
Authors: Tehrani N 
Published: February 2024

AbstractBackgroundOccupational Health Services (OHS) workers in the police are exposed to stressful and pressurized environments where they try to help employees deal with serious physical and mental health conditions.AimsThis study used psychological surveillance to identify the level of mental health conditions within each of the police OHS (POHS) roles and to identify whether it was possible to identify the main hazards and resilience factors related to these conditions.MethodsData on mental health conditions (anxiety, depression, post-traumatic stress disorder [PTSD] and secondary trauma) were gathered with questionnaires measuring lifestyle, coping skills, workability and illness behaviour. Personal information and average symptoms, hazards, and resilience factors were measured and compared between the POHS groups. Stepwise linear regression was used to identify the variable that explained the symptoms’ level.ResultsData were gathered from 251 POHS team members working in multidisciplinary services, including OH physicians, psychologists, advisors, nurses, technicians, well-being and administrators. The results showed that POHS teams are experiencing levels of symptoms significantly higher than those found in the general population and that OH counsellors had lower levels of symptoms and sickness absence than their colleagues. The stepwise regression identified managing workloads to be associated with lower symptom levels.ConclusionsThe findings illustrated the importance of a manageable workload, a stable, resilient personality and a positive attitude towards work. Using coping skills, including physical fitness, social support, involvement and getting enough sleep is associated with lower anxiety, depression, PTSD and secondary trauma symptoms.