bluuebunny/crossref_metadata_2025_split huggingface dataset:
SiPhyNetwork: An R package for simulating phylogenetic networks
Authors: Justison Joshua A. , Solis‐Lemus Claudia , Heath Tracy A. 
Published: May 2023

Abstract

Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow (e.g. introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account for these idiosyncrasies when constructing phylogenetic models. Existing phylogenetic‐network simulators for macroevolution are limited in the ways they model gene flow.

We present SiPhyNetwork, an R package for simulating phylogenetic networks under a birth–death‐hybridization process.

Our package unifies the existing birth–death‐hybridization models while also extending the toolkit for modelling gene flow. This tool can create patterns of reticulation such as hybridization, lateral gene transfer, and introgression.

Specifically, we model different reticulate events by allowing events to either add, remove or keep constant the number of lineages. Additionally, we allow reticulation events to be trait dependent, creating the ability to model the expanse of isolating mechanisms that prevent gene flow. This tool makes it possible for researchers to model many of the complex biological factors associated with gene flow in a phylogenetic context.
Standardized blood volume changes monitored by capnodynamic hemodynamic variables: An experimental comparative study in pigs
Authors: Karlsson Jacob , Hallbäck Magnus , Svedmyr Anders , Lönnqvist Per‐Arne , Wallin Mats 
Published: May 2023

AbstractBackgroundThe capnodynamic method, based on Volumetric capnography and differential Fick mathematics, assess cardiac output in mechanically ventilated subjects. Capnodynamic and established hemodynamic monitoring parameters' capability to depict alterations in blood volume were investigated in a model of standardized hemorrhage, followed by crystalloid and blood transfusion.MethodsTen anesthetized piglets were subjected to controlled hemorrhage (450 mL), followed by isovolemic crystalloid bolus and blood re‐transfusion. Intravascular blood volume, and all hemodynamic variables, were determined twice after each intervention. The investigated hemodynamic variables were: cardiac output and stroke volume for capnodynamics and pulse contour analysis, respectively, pulse pressure and stroke volume variability and mean arterial pressure. One‐way ANOVA and Tukey's test for multiple comparisons were used to identify significant changes. Trending was assessed by correlation and concordance.ResultConcordance against intravascular volume changes for capnodynamic cardiac output and stroke volume were 96 and 94%, with correlations r = .78 and .68, (p < .0001) with significant changes for 6 and 5 of the 6 measuring points, respectively. Mean arterial pressure and pulse pressure variation had a concordance of 85% and 87%, r = .67 (p < .0001) and r = −.45 (p < .0001), respectively, and both changed significantly for 3 of 6 measuring points. Pulse contour stroke volume variation, stroke volume and cardiac output, showed concordance and correlation of 76%, r = −.18 (p = .11), 63%, r = .28 (p = .01) and 50%, r = .31 (p = .007), respectively and significant change for 1, 1 and 0 of the measuring points, respectively.ConclusionCapnodynamic cardiac output and stroke volume did best depict the changes in intravascular blood volume. Pulse contour parameters did not follow volume changes in a reliable way.
Erythropoietin to treat anaemia in critical care patients: a multicentre feasibility study
Authors: Léger M. , Auchabie J. , Ferrandière M. , Parot‐Schinkel E. , Campfort M. , Rineau E. , Lasocki S. 
Published: May 2023

SummaryAnaemia is common and associated with poor outcomes during and after critical illness. The use of erythropoietin to treat such anaemia is controversial with older studies showing mixed results. In this study, we aimed to evaluate the feasibility of performing a large multicentre randomised controlled trial of erythropoietin in this setting. We randomly allocated patients staying in the ICU for ≥ 72 h with haemoglobin ≤ 120 g.l‐1 to either a weekly injection of erythropoietin (40,000 iu, maximum of five injections) or placebo (saline). The primary endpoint was feasibility (as measured by recruitment, randomisation and follow‐up rates, and protocol compliance). Secondary endpoints included biological efficacy and clinical outcomes. Forty‐two participants were recruited and randomly allocated, all participants received the allocated intervention, but one withdrew their consent and refused the use of their data, leaving 20 in the erythropoietin group and 21 in placebo group. Follow‐up was completed for all patients who survived. The overall recruitment rate was 73.7% with 8.4 participants recruited on average per month. The last haemoglobin measured before hospital discharge (or death) was similar between the groups with a mean (SD) haemoglobin of 107 (21) vs. 95 (25) g.l‐1, mean difference (95%CI) 11 (‐4–26), g.l‐1, p = 0.154. A large, multicentre randomised controlled trial of erythropoietin to treat anaemia in ICU patients is feasible and necessary to determine effects of erythropoietin on mortality in ICU anaemic patients.
Evaluation of adjusted international normalized ratio goal in patients with HeartMate 3 left ventricular assist devices
Authors: Sowder Amanda , Ather Ayesha , Birks Emma , Kolodziej Andrew , Malyala Rajasekhar , Sieg Adam , Schadler Aric , Unger Rachel , Guglin Maya , Kuan William 
Published: May 2023

AbstractBackgroundThe HeartMate3 left ventricular assist device (HM3 LVAD) has shown a low incidence of thrombosis, but bleeding risk is as high as 43%. We aim to describe the impact of lower international normalization ratio (INR) goal on clinical outcomes.MethodsIn February 2019, our tertiary care institution lowered INR goal in HM3 patients from manufacturer recommendations to 1.8–2.2 and retrospectively analyzed the data. Two cohorts were compared: patients with lower INR goal upon implant (De novo) and those with subsequently lowered INR goal (Adjusted). The Adjusted group also served as its own historical control. Both groups continued aspirin 81 milligrams daily per manufacturer recommendations. The primary outcomes were incidences of bleed and thrombosis events within 12 months. Secondary outcomes included survival free of disabling stroke or reoperation to remove or replace the device and Rosendaal time in therapeutic range (TTR) over 12 months.ResultsThirty‐one patients were evaluated for inclusion with 26 meeting criteria. Within 12 months, incidence of bleeding events was 25% and 28.6% in the De novo and Adjusted groups, respectively. Incidence of thrombotic events within 12 months was 0% in the De novo group and 7.1% in the Adjusted group. Twelve‐month survival free of disabling stroke or reoperation to remove or replace the device was higher over 12 months for patients in the De novo group (91.7% vs. 78.6%). Median 12‐month TTR was 36%, which was primarily attributable to subtherapeutic deviations.ConclusionsA lower INR goal may be safe when initiated De novo following implantation of the HM3. This study informs the need for larger prospective studies.
Attentional differences in audiovisual face perception between full‐ and preterm very low birthweight toddlers
Authors: Nakagawa Atsuko , Sukigara Masune , Nomura Kayo , Nagai Yukiyo , Miyachi Taishi 
Published: May 2023

AbstractAimTo investigate whether rightward attention to the mouth during audiovisual speech perception may be a behavioural marker for early brain development, we studied very preterm and low birthweight (VLBW) and typically developing (TD) toddlers.MethodsWe tested the distribution of gaze points in Japanese‐learning TD and VLBW toddlers when exposed to talking, silent and mouth moving faces at 12, 18 and 24 months (corrected age). Each participant was categorised based upon the area they gazed at most (Eye‐Right, Eye‐Left, Mouth‐Right, Mouth‐Left) per stimulus per age. A log‐linear model was applied to three‐dimensional contingency tables (region, side and group).ResultsVLBW toddlers showed fewer gaze points than TD toddlers. At 12 months, more VLBW toddlers than TD toddlers showed left attentional bias toward any one face; however, this difference in attention asymmetry receded somewhat by 24 months. In talking condition, TD toddlers showed right attentional bias from 12 to 24 months, whereas VLBW toddlers showed such bias upon reaching 24 months. Additionally, more TD toddlers than VLBW toddlers attended to the mouth.ConclusionDelays in exhibiting the attentional bias for an audiovisual face or general faces displayed by typically developing children might suggest differential developmental timing for hemispheric specialisation or dominance.
The homeless of urban India under COVID‐19 lockdown: Rethinking their rights and the role of public policy
Authors: Bhattacharjee Sujayita 
Published: May 2023

AbstractHomelessness comes with a slew of challenges and a never‐ending struggle for survival. This study examines the impact of the pandemic and lockdown on the homeless population of urban India. The study reflects on the experiences of the homeless in the major cities of India during the first wave of the pandemic as well as explores the aspect of their rights and the role of government policy in this regard. The methodology of the study is qualitative in nature, where secondary data collected from various sources such as news articles, blogs, books, journals, and reports are put to analysis for deriving the findings. The study reveals the sufferings of the homeless in the cities of Delhi, Mumbai, Kolkata, Bengaluru, and Chennai. Their fight is not merely with the SARS‐CoV‐2 virus but also with hunger, unemployment, and neglect faced by them. The study highlights the fact that their rights are being compromised due to drawbacks relating to policy implementation. The study concludes with certain suggestions such as, addressing the loopholes in policy implementations and creating sustainable livelihood opportunities.
CXCL14 immunoreactivity is localized in pituitary GH‐producing cells and in median eminence somatostatin‐containing fibres of the Japanese quail (Coturnix japonica)
Authors: Suzuki Hirohumi , Isobe Ami , Yamamoto Toshiharu 
Published: May 2023

AbstractThis is the first study to examine the distribution of a chemokine CXCL14‐like peptide in the pituitary and hypothalamus of an avian species, the Japanese quail (Coturnix japonica). We employed immunohistochemical techniques using a specific anti‐human CXCL14 antibody. CXCL14‐immunoreactive cells were detected in the caudal lobe of the pars distalis. CXCL14‐immunoreactive puncta were densely distributed in the external layer and sparsely distributed in the internal layer of the median eminence. CXCL14 staining was absent after pre‐absorption of the antibody with recombinant human CXCL14. All CXCL14‐immunoreactive cells corresponded to growth hormone (GH)‐producing cells in the caudal lobe. In addition, the majority of CXCL14‐immunoreactive puncta in the median eminence corresponded to somatostatin‐containing fibres. CXCL14 secreted from GH‐producing cells and somatostatin‐containing fibres may act as an inhibitor of GH release via an autocrine mechanism and neuroendocrine signalling, respectively.
Pathogenesis, clinical features and treatment of anti‐IgLON5 disease
Authors: Ono Yoya , Kimura Akio , Shimohata Takayoshi 
Published: May 2023

AbstractAnti‐immunoglobulin‐like cell adhesion molecule 5 (IgLON5) disease is an autoimmune encephalitis that targets the cell adhesion molecule, IgLON5. The disease presents with various clinical features, including sleep disorders, bulbar palsy, movement disorders, cognitive dysfunction and neuromuscular manifestations. Sleep disorders are characterized by parasomnias and sleep‐disordered breathing (stridor and sleep apnea). Bulbar palsy includes dysarthria, dysphagia, vocal cord paralysis and stridor. Movement disorders include a variety of symptoms and signs, such as chorea, dystonia, rigidity, tremor, myoclonus and myorhythmia. Cognitive dysfunction includes executive dysfunction, impairment of attention, and verbal and visual memory dysfunction. Neuromuscular manifestations include fasciculations in the tongue and peripheral muscles, limb weakness, and muscle atrophy. Some patients resemble those with neurodegenerative diseases, such as progressive supranuclear palsy or amyotrophic lateral sclerosis. On video polysomnography, undifferentiated non‐rapid eye movement sleep and poorly structured N2 sleep are characteristic. Brain magnetic resonance imaging and cerebrospinal fluid studies are often normal or non‐specific. Human leukocyte antigen testing shows that HLA‐DRB1*10:01‐DQB1*05:01 is highly associated with the disease. Pathologically, neuronal deposition of both hyperphosphorylated 3‐repeat and 4‐repeat tau isoforms, neuronal loss, and gliosis in the hypothalamus, brainstem tegmentum, and upper cervical cord are observed. Some patients are responsive to immunotherapies, such as steroids, intravenous immunoglobulin, plasma exchange therapy and rituximab. Factors associated with a favorable response to immunotherapies include early initiation of treatment, cerebrospinal fluid inflammation and immunoglobulin G1 (IgG1) predominance of IgLON5 antibody compared with immunoglobulin G4 (IgG4). Anti‐IgLON5 disease should be suspected in patients with atypical movement disorders complicated by sleep disturbances.
Ekzematisierte Psoriasis – eine häufige, aber oft vernachlässigte Variante der Plaque‐Psoriasis
Authors: Lauffer Felix , Eyerich Kilian 
Published: May 2023

ZusammenfassungPsoriasis ist eine der häufigsten chronisch‐entzündlichen Hauterkrankung, die mit systemischen Entzündungsreaktionen einhergeht und die Lebensqualität betroffener Patienten stark beeinträchtigt. In den letzten Jahren wurden mehrere hochwirksame Therapeutika für die Psoriasis zugelassen. In der Praxis kommt es jedoch bei einem hohen Anteil der Patienten nicht zu der in klinischen Studien beobachteten klinischen Verbesserung oder es kommt zu einem sekundären Wirkungsverlust. Dies kann möglicherweise auf bisher nicht erkannte Endotypen der Psoriasis zurückgeführt werden, die für die Wahl einer geeigneten Therapie eingehender charakterisiert werden müssen. Die ekzematisierte Psoriasis, die bei etwa 5–10% der Patienten mit Psoriasis auftritt, ist eine häufig vernachlässigte Variante der Psoriasis. Der Begriff „ekzematisierte Psoriasis“ bezieht sich auf Patienten, die unter einer Psoriasis leiden, die gewisse Ähnlichkeiten mit einem Ekzem aufweist. Betroffene Patienten haben oft einen starken Juckreiz und in Hautbiopsien lassen sich häufig eosinophile Granulozyten, Serumkrusten oder Spongiose nachweisen. Aus immunologischer Sicht werden bei der ekzematisierten Psoriasis möglicherweise zusätzliche Signalwege aktiviert, die für Ekzemreaktionen verantwortlich sind. Diese Übersichtsarbeit fasst die wichtigsten klinischen, histologischen und immunologischen Merkmale der ekzematisierten Psoriasis zusammen, schlägt diagnostische Kriterien vor und bewertet die aktuellen therapeutischen Optionen für die ekzematisierte Psoriasis.
Kidney protection with canagliflozin: A combined analysis of the randomizedCANVASprogram andCREDENCEtrials
Authors: Sridhar Vikas S. , Neuen Brendon L. , Fletcher Robert A. , Slee April , Ang Fernando G. , Rapattoni Wally , Arnott Clare , Cherney David Z. , Perkovic Vlado , Wheeler David C. , Levin Adeera 
Published: May 2023

AbstractAimIn the CANVAS Program and CREDENCE trials, the sodium glucose co‐transporter 2 inhibitor canagliflozin reduced the risk of cardiovascular and kidney events in patients with type 2 diabetes. The current study analysed a pooled population to ascertain the kidney protection provided by canagliflozin across the full spectrum of kidney parameters.MethodsThis post‐hoc pooled analysis of the CANVAS Program (N = 10 142) and CREDENCE trial (N = 4401), assessed the risk of the primary kidney composite (doubling of serum creatinine, end‐stage kidney disease, renal death), in all patients and subgroups defined by baseline estimated glomerular filtration rate (<30, 30 to <45, 45 to <60 and ≥60 ml/min/1.73 m2), albuminuria [<30, 30‐300, >300 mg/g (<3.39, 3.39‐33.9, >33.9 mg/mmol)] and 2012 Kidney Disease: Improving Global Outcomes (KDIGO) classification of chronic kidney disease (low/moderate, high and very high risk).ResultsIn the overall population, the risk for the primary kidney composite outcome was 37% lower in the canagliflozin group versus placebo (HR: 0.63; 95% CI: 0.53, 0.77;p < .001). There was no evidence of heterogeneity in the kidney protective effects of canagliflozin across a range of kidney risks when stratified by baseline estimated glomerular filtration rate, albuminuria or KDIGO risk category (allpinteraction > .05). A statistically significant risk reduction of the primary kidney composite outcome was sustained by approximately 18 months after randomization.ConclusionsThese results emphasize a critical role of canagliflozin in kidney protection across a broad spectrum of participants with type 2 diabetes with varying levels of kidney function.
Changes to relative stand composition after almost 50 years of Heterobasidion root disease in California true fir and pine forests
Authors: Flores D. Alexander , Poloni Adrian L. , Frankel Susan J. , Cobb Richard C. 
Published: May 2023

AbstractThe Agaricomycete Heterobasidion annosum sensu lato (s.l.), a species complex of fungal pathogens, causes root and butt rot on conifers throughout the northern hemisphere, thereby shaping structure, composition, and evolution of vast and diverse forest ecosystems. We analyze forest change 48–49 years following Heterobasidion root disease emergence in 63 permanent plots first established in 1970–1972 and measured at least once every decade through 2020. We use this dataset to infer the long‐term consequences of Heterobasidion root disease in a set of common forest types that reflect some of the most important hosts for this set of diseases in western North America. We contrasted three host–pathogen systems located within the Sierra Nevada, southern Cascades Mountain Range and the Modoc Plateau: (1) H. irregulare in host communities dominated by several Pinus (pine) species and Calocedrus decurrens (incense cedar) in Yosemite Valley, on the Sierra Nevada Range western slope; (2) H. irregulare in a largely single species (Pinus jeffreyi) host disease system on the eastern slopes of the Sierra Nevada and southern Cascades as well as the Modoc Plateau; and (3) H. occidentale—also on the western slope of the Sierra Nevada—in stands with a mixture of susceptible Abies (true fir) and a diversity of non‐hosts for this Heterobasidion species. Approximately 50 years after disease emergence, relative basal area and stem density were significantly reduced within disease centres in all three pathosystems, but changes to forest composition and relative species dominance were determined by pre‐disease host and non‐host diversity. In the western‐slope H. occidentale system, the disease increased the dominance of non‐susceptible species, Pinus species and C. decurrens. In the multi‐genus Yosemite pathosystem, H. irregulare did not significantly shift species dominance, and as expected, species shifts did not occur in the largely single‐genus eastern‐slope forests. In these widespread California forest ecosystems, two factors appeared to determine forest conditions almost 50 years after Heterobasidion root disease monitoring: the size of the disease centre and the initial diversity of non‐hosts. Along with pathogen species, these factors appear to affect the local severity of disease as well as the degree of species shifts relative to initial plot compositions, reaffirming host susceptibility classifications associated with these forest types.
A debate on the neuronal origin of focal seizures
Authors: Wenzel Michael , Huberfeld Gilles , Grayden David B. , de Curtis Marco , Trevelyan Andrew J. 
Published: May 2023

AbstractA critical question regarding how focal seizures start is whether we can identify particular cell classes that drive the pathological process. This was the topic for debate at the recent International Conference for Technology and Analysis of Seizures (ICTALS) meeting (July 2022, Bern, CH) that we summarize here. The debate has been fueled in recent times by the introduction of powerful new ways to manipulate subpopulations of cells in relative isolation, mostly using optogenetics. The motivation for resolving the debate is to identify novel targets for therapeutic interventions through a deeper understanding of the etiology of seizures.
Code‐mixed Hindi‐English text correction using fuzzy graph and word embedding
Authors: Jain Minni , Jindal Rajni , Jain Amita 
Published: May 2023

AbstractInteraction via social media involves frequent code‐mixed text, spelling errors and noisy elements, which creates a bottleneck in the performance of natural language processing applications. This proposed work is the first approach for code‐mixed Hindi‐English social media text that comprises language identification, detection and correction of non‐word (Out of Vocabulary) errors as well as real‐word errors occurring simultaneously. Each identified language (Devanagari Hindi, Roman Hindi, and English) has its own complexities and challenges. Errors are detected individually for each language and a suggestive list of the erroneous words is created. After this, a fuzzy graph between different words of the suggestive lists is generated using various semantic relations in Hindi WordNet. Word embeddings and Fuzzy graph‐based centrality measures are used to find the correct word. Several experiments are performed on different social media datasets taken from Instagram, Twitter, YouTube comments, Blogs, and WhatsApp. The experimental results demonstrate that the proposed system corrects out‐of‐vocabulary words as well as real‐word errors with a maximum recall of 0.90 and 0.67, respectively for Dev_Hindi and 0.87 and 0.66, respectively for Rom_Hindi. The proposed method is also applied for state‐of‐art sentiment analysis approaches where the F1‐score has been visibly improved.