Miracle-dz/UniFAR-FTUs huggingface dataset:
New Paratethyan dwarf baleen whales mark the origin of cetotheres

Background Family Cetotheriidae sensu stricto and several closely related taxa comprise the Cetotherioidea and represent a lineage of Neogene baleen whales that includes the smallest edentulous baleen whales in Earth history. Most of known cetotheriids came from the Late Miocene to Quaternary, and the earliest records from the latest Middle Miocene. The Paratethys region shows a great diversity of Middle to Late Miocene cetotheriids. That includes nominative taxon of the family, Cetotherium rathkii, and this suggests that the earliest cetotheriids may have lived in that region. Materials and methods Here, Ciuciulea davidi, a new genus and species from the Middle Miocene of southeastern Europe, is described as the chronologically earliest and earliest diverging member of Cetotheriidae. Also, a new specimen of Otradnocetus, a basal Cetotherioidea sensu Gol’din & Steeman, 2015 is identified from the Late Miocene deposits of Caucasus and compared with Otradnocetus virodovi from the Middle Miocene of the same region. Results and discussion Ciuciulea davidi is a dwarf whale displaying primitive traits: posterior ends of facial bones forming a single transverse line, a narrow occipital shield, and a relatively long interparietal region. Meanwhile, it shares some cetotheriid apomorphies: posteriorly telescoped wedge-shaped facial bones and an ovoid tympanic bulla with shallow lateral and medial furrows, a short anterior lobe and a short sigmoid process. Phylogenetic analysis suggests that Parietobalaena and Otradnocetus are branches diverging before the clade Cetotheriidae + Neobalaenidae. This is confirmed by the stepwise evolution of the anatomy of the squamosal, mandible, and ear bones across these groups. The re-described juvenile specimen of Otradnocetus differs from O. virodovi in the more primitive anatomy of the mandible and the autapomorphic anatomy of the humerus. Records of the earliest cetotheriids and related taxa in the Paratethys support the idea that this could be the region where Cetotheriidae evolved before their worldwide dispersal and radiation.
Better Oral Hygiene Habits Are Associated With a Lower Incidence of Peritoneal Dialysis‐Related Peritonitis

Some peritoneal dialysis (PD)‐related peritonitis cases are thought to be caused by the pathogens in the oral cavity; however, the relationship between peritonitis and oral hygiene habits is unclear. In this study, we retrospectively examined the relationship between oral hygiene habits and peritonitis in patients who agreed to a questionnaire survey. Of the 75 patients, 37 patients developed PD‐related peritonitis during the observation period. Peritonitis‐free survival was significantly higher in patients who spent more time on oral hygiene daily and in patients who replaced their toothbrush more frequently (P < 0.05). According to multivariable analysis, increased daily oral hygiene duration and more frequent toothbrush replacement were associated with a significantly (P < 0.01) lower risk for peritonitis (hazard ratio [HR] 0.37 [95% CI, 0.18–0.77] and HR 0.35 [95% CI, 0.17–0.70], respectively). In conclusion, PD patients with superior oral hygiene habits showed a lower risk for PD‐related peritonitis.
Effects of prolonged exposure to feedback delay on the qualitative subjective experience of virtual reality

When interacting with virtual environments, feedback delays between making a movement and seeing the visual consequences of that movement are detrimental for the subjective quality of the VR experience. Here we used standard measures of subjective experiences such as ownership, agency and presence to investigate whether prolonged exposure to the delay, and thus the possibility to adapt to it, leads to the recovery of the qualitative experience of VR. Participants performed a target-tracking task in a Virtual Reality environment. We measured the participants’ tracking performance in terms of spatial and temporal errors with respect to the target in both No-Delay and Delay conditions. Additionally, participants rated their sense of “ownership” of holding a virtual tool, agency and presence on each trial using sliding scales. These single trial ratings were compared to the results of the more traditional questionnaires for ownership and agency and presence for both No-Delay and Delay conditions. We found that the participants’ sliding scales ratings corresponded very well to the scores obtained from the traditional questionnaires. Moreover, not only did participants behaviourally adapt to the delay, their ratings of ownership and agency significantly improved with prolonged exposure to the delay. Together the results suggest a tight link between the ability to perform a behavioural task and the subjective ratings of ownership and agency in virtual reality.
Contribution of the TNF-&agr; (Tumor Necrosis Factor-&agr;)–TNF-Rp55 (Tumor Necrosis Factor Receptor p55) Axis in the Resolution of Venous Thrombus

Objective— Deep vein thrombosis results from a combination of risk factors including genetic conditions, obesity, drugs, pregnancy, aging, and malignancy. We examined pathophysiological roles of the TNF-&agr; (tumor necrosis factor-&agr;)–TNF-Rp55 (tumor necrosis factor receptor p55) axis in thrombus resolution using Tnfrp55−/− (TNF-Rp55–deficient) mice. Approach and Results— On ligating the inferior vena cava of wild-type (WT) mice, venous thrombi formed and grew progressively until 5 days but shrunk to <50% of the thrombus weight at day 14. Concomitantly, inferior vena cava ligation enhanced intrathrombotic gene expression of Tnfa and Tnfrp55, and intrathrombotic macrophages expressed both TNF-&agr; and TNF-Rp55 proteins. In Tnfrp55−/− mice treated with the same manner, thrombus formed at a similar rate for 5 days, but shrinking was delayed compared with WT mice. Moreover, the blood flow recovery in thrombosed inferior vena cava was suspended in Tnfrp55−/− mice compared with WT mice. Intrathrombotic Plau (urokinase-type plasminogen activator), Mmp2 (matrix metalloproteinase 2), and Mmp9 (matrix metalloproteinase 9) mRNA expression was significantly reduced in Tnfrp55−/− mice, compared with WT ones. Supportingly, the administration of anti–TNF-&agr; antibody or TNF-&agr; inhibitor (etanercept) delayed the thrombus resolution in WT mice. Furthermore, TNF-&agr; treatment enhanced gene expression of Plau, Mmp2, and Mmp9 in WT macrophages but not Tnfrp55−/− macrophages. These effects were significantly suppressed by ERK (extracellular signal regulated kinase) and NF-&kgr;B (nuclear factor-kappa B) inhibitors. Therefore, the lack of TNF-Rp55 has detrimental roles in the thrombus resolution by suppressing PLAU, MMP-2, and MMP-9 expression. In contrast, TNF-&agr; administration accelerated thrombus resolution in WT but not Tnfrp55−/− mice. Conclusions— The TNF-&agr;–TNF-Rp55 axis may have essential roles in the resolution of venous thrombus in mice.
Dynamic Automatic Differentiation of GPU Broadcast Kernels

We show how forward-mode automatic differentiation (AD) can be employed within larger reverse-mode computations to dynamically differentiate broadcast operations in a GPU-friendly manner. Our technique fully exploits the broadcast Jacobian's inherent sparsity structure, and unlike a pure reverse-mode approach, this "mixed-mode" approach does not require a backwards pass over the broadcasted operation's subgraph, obviating the need for several reverse-mode-specific programmability restrictions on user-authored broadcast operations. Most notably, this approach allows broadcast fusion in primal code despite the presence of data-dependent control flow. We discuss an experiment in which a Julia implementation of our technique outperformed pure reverse-mode TensorFlow and Julia implementations for differentiating through broadcast operations within an HM-LSTM cell update calculation.
Dynamic cerebral autoregulation is impaired in Veterans with Gulf War Illness: A case-control study

Neurological dysfunction has been reported in Gulf War Illness (GWI), including abnormal cerebral blood flow (CBF) responses to physostigmine challenge. However, it is unclear whether the CBF response to normal physiological challenges and regulation is similarly dysfunctional. The goal of the present study was to evaluate the CBF velocity response to orthostatic stress (i.e., sit-to-stand maneuver) and increased fractional concentration of carbon dioxide. 23 cases of GWI (GWI+) and 9 controls (GWI) volunteered for this study. Primary variables of interest included an index of dynamic autoregulation and cerebrovascular reactivity. Dynamic autoregulation was significantly lower in GWI+ than GWI- both for autoregulatory index (2.99±1.5 vs 4.50±1.5, p = 0.017). In addition, we observed greater decreases in CBF velocity both at the nadir after standing (-18.5±6.0 vs -9.8±4.9%, p = 0.001) and during steady state standing (-5.7±7.1 vs -1.8±3.2%, p = 0.042). In contrast, cerebrovascular reactivity was not different between groups. In our sample of Veterans with GWI, dynamic autoregulation was impaired and consistent with greater cerebral hypoperfusion when standing. This reduced CBF may contribute to cognitive difficulties in these Veterans when upright.
Fetal Medicine Foundation reference ranges for umbilical artery and middle cerebral artery pulsatility index and cerebroplacental ratio

To develop gestational age‐based reference ranges for the pulsatility index in the umbilical artery (UA‐PI) and fetal middle cerebral artery (MCA‐PI) and the cerebroplacental ratio (MCA‐PI/UA‐PI), and to examine the maternal characteristics and medical history that affect these measurements.
Pathophysiology of essential hypertension: an update

ABSTRACT Introduction: Hypertension is caused by increased cardiac output and/or increased peripheral resistance. Areas covered: The various mechanisms affecting cardiac output/peripheral resistance involved in the development of essential hypertension are covered. These include genetics; sympathetic nervous system overactivity; renal mechanisms: excess sodium intake and pressure natriuresis; vascular mechanisms: endothelial cell dysfunction and the nitric oxide pathway; hormonal mechanisms: the renin-angiotensin-aldosterone system (RAAS); obesity, obstructive sleep apnea (OSA); insulin resistance and metabolic syndrome; uric acid; vitamin D; gender differences; racial, ethnic, and environmental factors; increased left ventricular ejection force and hypertension and its association with increased basal sympathetic activity – cortical connections. Expert commentary: Maximum association of hypertension is found with sympathetic overactivity which is directly or indirectly involved in different mechanisms of hypertension including RAAS, OSA, obesity, etc. It is not overt sympathetic activity but disturbed basal sympathetic tone. Basal sympathetic tone arises from hypothalamus; possibly affected by cortical influences. Therefore, hypertension is not merely a disease of circulatory system alone. Its pathogenesis involves alteration in ANS (autonomic nervous system) and likely in cortical-hypothalamic connections. Assessment of ANS and cortical-hypothalamic connections may be required for better understanding of hypertension.
Elevated Neutrophil and Presence of Intracranial Artery Stenosis Increase the Risk of Recurrent Stroke

Background and Purpose— The association of neutrophil and intracranial artery stenosis (ICAS) with the prognosis of stroke is uncertain. This study evaluated the relationship between neutrophil levels with and without ICAS and the prognosis of patients with minor stroke or transient ischemic attack. Methods— Data from the CHANCE trial (Clopidogrel in High-Risk Patients With Acute Nondisabling Cerebrovascular Events) was reviewed. Patients were divided into 4 groups according to the dichotomy of neutrophil counts and status of ICAS. The primary outcome was a new stroke (ischemic or hemorrhagic), and secondary outcomes included a new composite vascular event (stroke, myocardial infarction, or cardiovascular death) and ischemic stroke. Safety outcome was any hemorrhage at 90 days. The association between neutrophil counts with and without ICAS and risk of any outcome was analyzed by Cox regression models. Results— Of 1034 patients included in this subgroup analysis, 91 had recurrent strokes. Compared with the lower neutrophil levels without ICAS, higher neutrophil levels with ICAS significantly increased the risk of stroke recurrence (adjusted hazard ratio, 2.26; 95% CI, 1.19–4.31; P=0.01) and composite outcome (adjusted hazard ratio, 1.98; 95% CI, 1.06–3.67; P=0.03). However, there was no safety issue. Conclusions— Concomitant presence of higher neutrophil levels and ICAS was associated with the increased risk of stroke recurrence, and combined adverse outcome events in patients already had minor ischemic stroke or high-risk transient ischemic attack. Clinical Trial Registration— URL: https://www.clinicaltrials. gov. Unique identifier: NCT00979589.
Geriatric CO-mAnagement for Cardiology patients in the Hospital (G-COACH): study protocol of a prospective before-after effectiveness-implementation study

Introduction Although the majority of older patients admitted to a cardiology unit present with at least one geriatric syndrome, guidelines on managing heart disease often do not consider the complex needs of frail older patients. Geriatric co-management has demonstrated potential to improve functional status, and reduce complications and length of stay, but evidence on the effectiveness in cardiology patients is lacking. This study aims to determine if geriatric co-management is superior to usual care in preventing functional decline, complications, mortality, readmission rates, reducing length of stay and improving quality of life in older patients admitted for acute heart disease or for transcatheter aortic valve implantation, and to identify determinants of success for geriatric co-management in this population. Methods and analysis This prospective quasi-experimental before-and-after study will be performed on two cardiology units of the University Hospitals Leuven in Belgium in patients aged ≥75 years. In the precohort (n=227), usual care will be documented. A multitude of implementation strategies will be applied to allow for successful implementation of the model. Patients in the after cohort (n=227) will undergo a comprehensive geriatric assessment within 24 hours of admission to stratify them into one of three groups based on their baseline risk for developing functional decline: low-risk patients receive proactive consultation, high-risk patients will be co-managed by the geriatric nurse to prevent complications and patients with acute geriatric problems will receive an additional medication review and co-management by the geriatrician. Ethics and dissemination The study protocol was approved by the Medical Ethics Committee UZ Leuven/KU Leuven (S58296). Written voluntary (proxy-)informed consent will be obtained from all participants at the start of the study. Dissemination of results will be through articles in scientific and professional journals both in English and Dutch and by conference presentations. Trial registration number NCT02890927.
New Genomic Approaches to Enhance Biomass Degradation by the Industrial Fungus Trichoderma reesei

The filamentous fungi Trichoderma reesei is one of the most well-studied cellulolytic microorganisms. It is the most important fungus for the industrial production of enzymes to biomass deconstruction being widely used in the biotechnology industry, mainly in the production of biofuels. Here, we performed an analytic review of the holocellulolytic system presented by T. reesei as well as the transcriptional and signaling mechanisms involved with holocellulase expression in this fungus. We also discuss new perspectives about control of secretion and cellulase expression based on RNA-seq and functional characterization data of T. reesei growth in different carbon sources, which comprise glucose, cellulose, sophorose, and sugarcane bagasse.
Mechanical behavior of shark vertebral centra at biologically relevant strains

ABSTRACT Cartilaginous shark skeletons experience axial deformation at the intervertebral joints, but also within the mineralized cartilaginous centrum, which can compress to between 3% and 8% of its original length in a free-swimming shark. Previous studies have focused on shark centra mechanical properties when loaded to failure; our goal was to determine properties when compressed to a biologically relevant strain. We selected vertebrae from six shark species and from the anterior and posterior regions of the vertebral column. Centra were X-radiographed to measure double cone proportion and apex angles, and were mechanically tested at three displacement rates to 4% strain. We determined the variation in toughness and stiffness of vertebral centra among shark species and ontogenetic stages, testing strain rates, and compared anterior and posterior regions of the vertebral column. Our results suggest that toughness and stiffness, which are positively correlated, may be operating in concert to support lateral body undulations, while providing efficient energy transmission and return in these swift-swimming apex predators. We analyzed the contribution of double cone proportion and apex angle to centra mechanical behavior. We found that the greatest stiffness and toughness were in the youngest sharks and from the posterior body, and there was significant interspecific variation. Significant inverse correlations were found between mechanical properties and double cone apex angle suggesting that properties can be partially attributed to the angle forming the double cone apex. These comparative data highlight the importance of understanding cartilaginous skeleton mechanics under a wide variety of loading conditions representative of swimming behaviors seen in the wild. Summary: When compressed to biologically relevant strains, cartilaginous vertebral centra stiffness and toughness vary among Carcharhiniformes and Lamniformes sharks, anterior and posterior body regions, ontogenetic groupings and strain rates.
Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing

The Eurasian perch (Perca fluviatilis) is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are rather limited. In this work, we report de novo assembly and annotation of the whole genome sequence of perch. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a draft perch genome ∼1.0 Gbp assembly (scaffold N50 = 6.3 Mb; the longest individual scaffold of 29.3 Mb; BUSCO completeness of 88.0%), which included 281.6 Mb of putative repeated sequences. The perch genome assembly presented here, generated from small amount of starting material (0.75 ng) and a single linked-read library, is highly continuous and considerably more complete than the currently available draft of P. fluviatilis genome. A total of 23,397 protein-coding genes were predicted, 23,171 (99%) of which were annotated functionally from either sequence homology or protein signature searches. Linked-read technology enables fast, accurate and cost-effective de novo assembly of large non-model eukaryote genomes. The highly continuous assembly of the Eurasian perch genome presented in this study will be an invaluable resource for a range of genetic, ecological, physiological, ecotoxicological, functional and comparative genomic studies in perch and other fish species of the Percidae family.
Inhibition enhances spatially-specific calcium encoding of synaptic input patterns in a biologically constrained model

Synaptic plasticity, which underlies learning and memory, depends on calcium elevation in neurons, but the precise relationship between calcium and spatiotemporal patterns of synaptic inputs is unclear. Here, we develop a biologically realistic computational model of striatal spiny projection neurons with sophisticated calcium dynamics, based on data from rodents of both sexes, to investigate how spatiotemporally clustered and distributed excitatory and inhibitory inputs affect spine calcium. We demonstrate that coordinated excitatory synaptic inputs evoke enhanced calcium elevation specific to stimulated spines, with lower but physiologically relevant calcium elevation in nearby non-stimulated spines. Results further show a novel and important function of inhibition—to enhance the difference in calcium between stimulated and non-stimulated spines. These findings suggest that spine calcium dynamics encode synaptic input patterns and may serve as a signal for both stimulus-specific potentiation and heterosynaptic depression, maintaining balanced activity in a dendritic branch while inducing pattern-specific plasticity.
Clinicopathological features of hydrophilic polymer emboli in Japanese autopsy cases

Hydrophilic polymer is used on multiple endovascular devices to decrease friction between these devices and vessel walls. Although it can prevent medical device‐related complications, hydrophilic polymer emboli (HPE) has recently been established as a potentially fatal iatrogenic phenomenon. HPE can cause tissue injury in numerous sites, including the brain, heart, lung, skin, and intestines. Most HPE reports have been from Europe and the USA. Therefore, we investigated the frequency, site distribution, and degree of tissue injury of HPE in 227 Japanese autopsy cases. HPE was noted in 3.1% (7/227 cases), and was only found in the lung or heart. There were no cases with tissue injury, such as vasculopathy, ischemia or infarction, associated with HPE. This is the first series study of HPE in Japanese autopsy cases. Unlike in reports from Europe and USA, HPE was only seen in the lung or heart and did not injure the surrounding tissue.