bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Polygenic Background on the Clinical Presentation of Familial Hypercholesterolemia
Authors: Trinder Mark , Cermakova Lubomira , Ruel Isabelle , Baass Alexis , Paquette Martine , Wang Jian , Kennedy Brooke A. , Hegele Robert A. , Genest Jacques , Brunham Liam R. 
Published: May 2024

BACKGROUND:
Heterozygous familial hypercholesterolemia (FH) is among the most common genetic conditions worldwide that affects ≈ 1 in 300 individuals. FH is characterized by increased levels of low-density lipoprotein cholesterol (LDL-C) and increased risk of coronary artery disease (CAD), but there is a wide spectrum of severity within the FH population. This variability in expression is incompletely explained by known risk factors. We hypothesized that genome-wide genetic influences, as represented by polygenic risk scores (PRSs) for cardiometabolic traits, would influence the phenotypic severity of FH.

METHODS:
We studied individuals with clinically diagnosed FH (n=1123) from the FH Canada National Registry, as well as individuals with genetically identified FH from the UK Biobank (n=723). For all individuals, we used genome-wide gene array data to calculate PRSs for CAD, LDL-C, lipoprotein(a), and other cardiometabolic traits. We compared the distribution of PRSs in individuals with clinically diagnosed FH, genetically diagnosed FH, and non-FH controls and examined the association of the PRSs with the risk of atherosclerotic cardiovascular disease.

RESULTS:
Individuals with clinically diagnosed FH had higher levels of LDL-C, and the incidence of atherosclerotic cardiovascular disease was higher in individuals with clinically diagnosed compared with genetically identified FH. Individuals with clinically diagnosed FH displayed enrichment for higher PRSs for CAD, LDL-C, and lipoprotein(a) but not for other cardiometabolic risk factors. The CAD PRS was associated with a risk of atherosclerotic cardiovascular disease among individuals with an FH-causing genetic variant.

CONCLUSIONS:
Genetic background, as expressed by genome-wide PRSs for CAD, LDL-C, and lipoprotein(a), influences the phenotypic severity of FH, expanding our understanding of the determinants that contribute to the variable expressivity of FH. A PRS for CAD may aid in risk prediction among individuals with FH.
3DVascNet: An Automated Software for Segmentation and Quantification of Mouse Vascular Networks in 3D
Authors: Narotamo Hemaxi , Silveira Margarida , Franco Cláudio A. 
Published: May 2024

BACKGROUND:
Analysis of vascular networks is an essential step to unravel the mechanisms regulating the physiological and pathological organization of blood vessels. So far, most of the analyses are performed using 2-dimensional projections of 3-dimensional (3D) networks, a strategy that has several obvious shortcomings. For instance, it does not capture the true geometry of the vasculature and generates artifacts on vessel connectivity. These limitations are accepted in the field because manual analysis of 3D vascular networks is a laborious and complex process that is often prohibitive for large volumes.

METHODS:
To overcome these issues, we developed 3DVascNet, a deep learning–based software for automated segmentation and quantification of 3D retinal vascular networks. 3DVascNet performs segmentation based on a deep learning model, and it quantifies vascular morphometric parameters such as vessel density, branch length, vessel radius, and branching point density. We tested the performance of 3DVascNet using a large data set of 3D microscopy images of mouse retinal blood vessels.

RESULTS:
We demonstrated that 3DVascNet efficiently segments vascular networks in 3D and that vascular morphometric parameters capture phenotypes detected by using manual segmentation and quantification in 2 dimension. In addition, we showed that, despite being trained on retinal images, 3DVascNet has high generalization capability and successfully segments images originating from other data sets and organs.

CONCLUSIONS:
Overall, we present 3DVascNet, a freely available software that includes a user-friendly graphical interface for researchers with no programming experience, which will greatly facilitate the ability to study vascular networks in 3D in health and disease. Moreover, the source code of 3DVascNet is publicly available, thus it can be easily extended for the analysis of other 3D vascular networks by other users.
Myocardial Blood Flow Reserve, Microvascular Coronary Health, and Myocardial Remodeling in Patients With Aortic Stenosis
Authors: Alahdab Fares , Ahmed Ahmed I. , Nayfeh Malek , Han Yushui , Abdelkarim Ola , Alfawara Moath S. , Little Stephen H. , Reardon Michael J. , Faza Nadeen N. , Goel Sachin S. , Alkhouli Mohamad , Zoghbi William , Al‐Mallah Mouaz H. 
Published: May 2024

Background
Coronary microvascular function and hemodynamics may play a role in coronary circulation and myocardial remodeling in patients with aortic stenosis (AS). We aimed to evaluate the relationship between myocardial blood flow and myocardial function in patients with AS, no AS, and aortic valve sclerosis.

Methods and Results

We included consecutive patients who had resting transthoracic echocardiography and clinically indicated positron emission tomography myocardial perfusion imaging to capture their left ventricular ejection fraction, global longitudinal strain (GLS), and myocardial flow reserve (MFR). The primary outcome was major adverse cardiovascular event (all‐cause mortality, myocardial infarction, or late revascularization). There were 2778 patients (208 with aortic sclerosis, 39 with prosthetic aortic valve, 2406 with no AS, and 54, 49, and 22 with mild, moderate, and severe AS, respectively). Increasing AS severity was associated with impaired MFR (
P
<0.001) and GLS (
P
<0.001), even when perfusion was normal. Statistically significant associations were noted between MFR and GLS, MFR and left ventricular ejection fraction, and MFR and left ventricular ejection fraction reserve. After a median follow‐up of 349 (interquartile range, 116–662) days, 4 (7.4%), 5 (10.2%), and 6 (27.3%) patients experienced a major adverse cardiovascular event in the mild, moderate, and severe AS groups, respectively. In a matched‐control analysis, patients with mild‐to‐moderate AS had higher rates of impaired MFR (52.9% versus 39.9%;
P
=0.048) and major adverse cardiovascular event (11.8% versus 3.0%;
P
=0.002).

Conclusions
Despite lack of ischemia, as severity of AS increased, MFR decreased and GLS worsened, reflecting worse coronary microvascular health and myocardial remodeling. Positron emission tomography–derived MFR showed a significant independent correlation with left ventricular ejection fraction and GLS. Patients with prosthetic aortic valve showed a high prevalence of impaired MFR.
Federated Learning for Exploiting Annotators’ Disagreements in Natural Language Processing
Authors: Rodríguez-Barroso Nuria , Cámara Eugenio Martínez , Collados Jose Camacho , Luzón M. Victoria , Herrera Francisco 
Published: May 2024

Abstract
The annotation of ambiguous or subjective NLP tasks is usually addressed by various annotators. In most datasets, these annotations are aggregated into a single ground truth. However, this omits divergent opinions of annotators, hence missing individual perspectives. We propose FLEAD (Federated Learning for Exploiting Annotators’ Disagreements), a methodology built upon federated learning to independently learn from the opinions of all the annotators, thereby leveraging all their underlying information without relying on a single ground truth. We conduct an extensive experimental study and analysis in diverse text classification tasks to show the contribution of our approach with respect to mainstream approaches based on majority voting and other recent methodologies that also learn from annotator disagreements.
Computational Complexity of Natural Morphology Revisited
Authors: Senuma Hajime , Aizawa Akiko 
Published: May 2024

Abstract
This paper revisits a classical, yet fundamental, discussion of theoretical computational linguistics: the computational complexity of natural languages. Past studies have revealed that syntax, as observed in Swiss-German, is not weakly context-free. Concerning morphology, Culy (1985) employed a construction in Bambara to show that morphology is not weakly context-free; however, Manaster-Ramer (1988) pointed out that the Bambara case can be problematic because the wordhood of the construction is reliant on special tonal behaviors, and it is ambiguous whether the behaviors belong to the morphological domain. This raises doubts about whether the case can be considered a genuine morphological phenomenon. In this paper, we argue that Classical Ainu, a language we examine, also defies weak context-freeness at the morphological level. The construction we introduce is unambiguously morphological because this language’s valency-sensitive structure and valency-changing operations, such as noun incorporation, preclude its grammatical interpretation as syntactic.
Evaluating Correctness and Faithfulness of Instruction-Following Models for Question Answering
Authors: Adlakha Vaibhav , BehnamGhader Parishad , Lu Xing Han , Meade Nicholas , Reddy Siva 
Published: May 2024

Abstract
Instruction-following models are attractive alternatives to fine-tuned approaches for question answering (QA). By simply prepending relevant documents and an instruction to their input, these models can be adapted to various information domains and tasks without additional training. However, these models tend to produce verbose responses with supplementary information, which makes traditional QA metrics like exact match (EM) and F1 unreliable for accurately quantifying model performance. In this work, we evaluate instruction-following models along two fronts: 1) how well they satisfy user’s information need (correctness), and 2) whether they disseminate information supported by the provided knowledge (faithfulness). Guided by human evaluation and analysis, we highlight the shortcomings of traditional metrics for both correctness and faithfulness and propose simple token-overlap metrics that correlate highly with human judgments. Our analysis reveals that for correctness, instruction-following models perform comparably to models specifically fine-tuned for that task. However, they struggle to accurately judge the relevance of the provided knowledge and often hallucinate in their responses. We hope our work encourages more holistic evaluation of instruction-following models for QA. Our code and human annotation data is available at https://github.com/McGill-NLP/instruct-qa.
A Linguistic Muddle. Sextus’ Arguments against Universals at PH 2.227–8
Authors: Pecorari Michele 
Published: May 2024

Abstract
At Outlines of Pyrrhonism (PH) 2.227–8, Sextus Empiricus argues that certain entities which his adversaries hold to be one and the same for different individuals are in fact not. This he does by, among other things, considering the truth-value of sentences of which the subject is a common noun, thereby drawing an interesting connection between metaphysics and semantics. In this article, I provide a careful analysis of Sextus’ arguments at PH 2.227–8 and explore the origins and limits of such a connection. In particular, I argue that Sextus’ argument at PH 2.227 probably reflects a Stoic argument against Aristotelian essences, thereby relying on specifically Stoic doctrines about universals and common nouns, whereas his next argument at PH 2.228 targets accidents. If this is true, it follows that the overall structure of PH 2.227–8 fits well with the typically Aristotelian distinction between essence and accident.
Extreme genetic depletion upon postglacial colonization hampers determining the provenance of introduced palmate newt populations
Authors: Elfering Robin , Mannix Sophie , Allain Steve , Ambu Johanna , Crochet Pierre-André , van Doorn Loïc , Dufresnes Christophe , Jehle Robert , Julian Angela , Baird Fairlie Kirkpatrick , O’Brien David , Secondi Jean , Speybroeck Jeroen , Theodoropoulos Anagnostis , Stark Tariq , Wielstra Ben 
Published: May 2024

Abstract
MtDNA barcoding is regularly applied to determine the provenance of invasive species. Variation in spatial genetic structuring across a species’ range, typically high within glacial refugia and low in postglacially colonized areas, influences the precision of this approach. The palmate newt (Lissotriton helveticus) has been introduced north of its native range inside the Netherlands. We conduct mtDNA barcoding to try and retrace the origin of the introduced localities. A large increase in sample size, particularly focusing on temperate Europe, emphasizes that the palmate newt shows practically no genetic variation outside the Iberian Peninsula glacial refugium. While we find a haplotype previously only known from the Iberian Peninsula inside the native range in Belgium, the haplotype present in the introduced Dutch populations occurs widely throughout the native range north of the Iberian Peninsula. Although mtDNA barcoding can be a powerful tool in invasion biology, the palmate newt case exposes its limitations.
Gut microbiome and symptoms in females with irritable bowel syndrome: a cross-sectional analysis
Authors: Kamp K.J. , Plantinga A.M. , Cain K.C. , Burr R.L. , Tsai C.-S. , Wu Q. , So S.Y. , Badu S. , Savidge T. , Shulman R.J. , Heitkemper M.M. 
Published: May 2024

Abstract
Irritable bowel syndrome (IBS), a disorder of gut-brain interaction, is associated with abdominal pain and stool frequency/character alterations that are linked to changes in microbiome composition. We tested whether taxa differentially abundant between females with IBS vs healthy control females (HC) are associated with daily gastrointestinal and psychological symptom severity. Participants (age 18-50 year) completed a 3-day food record and collected a stool sample during the follicular phase. They also completed a 28-day diary rating symptom intensity; analysis focused on the three days after the stool sample collection. 16S rRNA gene sequencing was used for bacterial identification. Taxon abundance was compared between IBS and HC using zero-inflated quantile analysis (ZINQ). We found that females with IBS (n = 67) had greater Bacteroides abundance (q = 0.003) and lower odds of Bifidobacterium presence (q = 0.036) compared to HC (n = 46) after adjusting for age, race, body mass index, fibre intake, and hormonal contraception use. Intestimonas, Oscillibacter, and Phascolarctobacterium were more often present and Christensenellaceae R-7 group, Collinsella, Coprococcus 2, Moryella, Prevotella 9, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005, and Ruminococcaceae UCG-014 were less commonly present in IBS compared to HC. Despite multiple taxon differences in IBS vs HC, we found no significant associations between taxon presence or abundance and average daily symptom severity within the IBS group. This may indicate the need to account for interactions between microbiome, dietary intake, metabolites, and host factors.
Decadal Changes (1980–2021) of Shoreline and Mangrove Cover in Sundarban Delta, India, Using Remote Sensing and GIS
Authors: Biswas Sipra , Sarkar Kallol , Das Tapan Kumar 
Published: May 2024

Abstract
Being situated in the estuary of the flood-dominated Hooghly River system, the macrotidal Indian Sundarban Delta (ISD) has become one of the most complex, dynamic, and rapidly changing landforms on Earth’s surface. To study the horizontal areal shifting of shoreline and its impact on mangrove cover in the region, the U.S. Geological Survey (USGS) satellite data of 1980, 1990, 2000, 2010, and 2021 were used. Remote sensing and geographic information system (GIS) techniques were employed in the investigation. Simultaneous prograding and retrograding shoreline shifting was distinguished almost in all the parts, although sediment-starved eastern and macrotidally more active southern lobes experienced dominantly retreating shift, and the sediment-engorged western lobe was demonstrated to be more dynamic. Net areal change over north–south tracks followed the trend of decreasing accretion to increasing erosion while going from west to east, whereas that over west–east tracks followed the trend of exponentially increasing erosion while going from north to south. Overall accretion of ∼91 km2 in the ISD accounted for the augmentation of sparse vegetation of ∼13 km2, whereas ∼243 km2 erosion called for the depletion of sparse and moderate vegetation of ∼18 and ∼174 km2, respectively, over the 41-yr period. Various oceanographic and riparian forces and actions, episodic natural events, etc., vis-a-vis several anthropogenic interventions—all together contributed to such changes. The findings may help the coastal environmentalists, professionals, planners, decision-makers, and implementers in formulating and taking up of suitable strategic measures for integrated and effective coastal zone management in this estuarine wetland forest.
Validation of Doppler Wind Lidar Measurements with an Uncrewed Aircraft System (UAS) in the Daytime Atmospheric Boundary Layer
Authors: Boventer Jakob , Bramati Matteo , Savvakis Vasileios , Beyrich Frank , Kayser Markus , Platis Andreas , Bange Jens 
Published: May 2024

Abstract
One of the most widely used systems for wind speed and direction observations at meteorological sites is based on Doppler wind lidar (DWL) technology. The wind vector derivation strategies of these instruments rely on the assumption of stationary and homogeneous horizontal wind, which is often not the case over heterogeneous terrain. This study focuses on the validation of two DWL systems, operated by the German Weather Service [Deutscher Wetterdienst (DWD)] and installed at the boundary layer field site Falkenberg (Lindenberg, Germany), with respect to measurements from a small, fixed-wing uncrewed aircraft system (UAS) of the type Multi-Purpose Airborne Sensor Carrier (MASC-3). A wind vector intercomparison at an altitude range from 100 to 500 m between DWL and UAS is performed, after a quality control of the aircraft’s data accuracy against a cup anemometer and wind vane mounted on a meteorological mast also operating at the location. Both DWL systems exhibit an overall root-mean-square difference in the wind vector retrieval of less than 22% for wind speed and lower than 18° for wind direction. The enhancement or deterioration of these statistics is analyzed with respect to scanning height and atmospheric stability. The limitations of this type of validation approach are highlighted and accounted for in the analysis.
New Anatomic Anterolateral Ligament Reconstruction Used in a Complex Revision ACL Reconstruction
Authors: Tollefson Luke V. , Kennedy Nicholas I. , LaPrade Robert F. 
Published: May 2024

Background: Anterior cruciate ligament reconstructions (ACLRs) are performed to restore knee biomechanics, increase knee stability, and slow the progression of osteoarthritis. After ACLRs, many patients still have residual anterolateral instability which is a risk factor for ACL graft failure. An anterolateral ligament reconstruction (ALLR) attempts to restore the native function of the anterolateral complex to augment the ACL. Performing an ALLR with an ACLR has been reported to reduce symptoms of instability and improve clinical outcomes. Indications: While no definitive indication for an ALLR has been set, current considerations include high posterior tibial slope >12°, revision ACLR, high-grade pivot shift, skeletally immature patients, hyperlaxity, and patients in high-level sports. Technique Description: The preoperative assessment includes a thorough physical examination with special attention paid to rotational laxity assessed via the pivot-shift examination. Imaging should include standard radiographic series (anteroposterior, posteroanterior flexion, lateral, and sunrise views), long-leg mechanical axis views to assess coronal plane alignment and standing lateral ACL stress radiographs to assess sagittal alignment and objective instability. The iliotibial band ALLR graft is harvested first. An 8-cm long by 1-cm wide strip of the inferior iliotibial band is harvested in a standard fashion, leaving the distal aspect attached to Gerdy’s tubercle. An anchor is placed centered upon the native ALL distal tibial insertion. The native ALL femoral origin is identified at 4.7 mm posterior and proximal to the fibular collateral ligament, and a second suture anchor is placed at this point. Final fixation is performed after the final fixation of the ACLR graft. Results: A study by Pioger et al reported that patients with ACLR and ALLR had significantly less reoperation rate than patients with isolated ACLR, 8.9% versus 20.5% respectively. Lee et al found that a revision ACLR in combination with an ALLR was effective in reducing rotational laxity, which was assessed by the pivot-shift test. Discussion: We describe a technique for a new anatomic ALLR using the iliotibial band that attempts to restore the native ALL anatomy. This surgical technique effectively restores rotational laxity and improves knee stability. Patient Consent Disclosure Statement: The author(s) attests that consent has been obtained from any patient(s) appearing in this publication. If the individual may be identifiable, the author(s) has included a statement of release or other written form of approval from the patient(s) with this submission for publication.
Non-arterial line cardiac output calculation misclassifies exercise pulmonary hypertension and increases risk of data loss particularly in black, scleroderma and Raynaud's patients during invasive exercise testing
Authors: Campedelli Luiz , Nouraie S. Mehdi , Risbano Michael G. 
Published: May 2024

BackgroundThe direct Fick principle is the standard for calculating cardiac output (CO) to detect CO-dependent conditions like exercise pulmonary hypertension (ePH). Fick COarterialincorporates arterial haemoglobin (Hba) and oxygen saturation (SaO2) with oxygen consumption from exercise testing, while Fick COnon-arterialsubstitutes mixed venous haemoglobin (Hbmv) and peripheral oxygen saturation (SpO2) in the absence of an arterial line. The decision to employ an arterial catheter for exercise testing varies, and discrepancies in oxygen saturation and haemoglobin between arterial and non-arterial methods may lead to differences in Fick CO, potentially affecting ePH classification.MethodsWe performed a retrospective analysis of 296 consecutive invasive cardiopulmonary exercise testing (iCPET) studies comparing oxygen saturation from pulse oximetry (SpO2) and radial arterial (SaO2), Hbaand Hbmv, and CO calculated with arterial (COarterial) and non-arterial (COnon-arterial) values. We assessed the risk of misclassification of pre- and post-capillary ePH and data loss due to inaccurateSpO2.ResultsWhen considering all stages from rest to peak exercise, Hbaand Hbmvdemonstrated high correlation, whileSpO2andSaO2as well as COarterialand COnon-arterialdemonstrated low correlation. Data loss was significantly higher across all stages of exercise forSpO2(n=346/1926 (18%)) compared toSaO2(n=17/1923 (0.88%)). We found that pre- and post-capillary ePH were misclassified as COnon-arterialdata (n=7/41 (17.1%) and n=2/23 (8.7%), respectively). Patients with scleroderma and/or Raynaud's (n=11/33 (33.3%)) and black patients (n=6/19 (31.6%)) had moreSpO2data loss.ConclusionReliance uponSpO2during invasive exercise testing results in the misclassification of pre- and post-capillary ePH, and unmeasurableSpO2for black, scleroderma and Raynaud's patients can preclude accurate exercise calculations, thus limiting the diagnostic and prognostic value of invasive exercise testing without an arterial line.