Miracle-dz/UniFAR-FTUs huggingface dataset:
Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics

Rapid advances in spatial transcriptomics (ST) have revolutionized the interrogation of spatial heterogeneity and increase the demand for comprehensive methods to effectively characterize spatial domains. As a prerequisite for ST data analysis, spatial domain characterization is a crucial step for downstream analyses and biological implications. Here we propose a prior-based self-attention framework for spatial transcriptomics (PAST), a variational graph convolutional autoencoder for ST, which effectively integrates prior information via a Bayesian neural network, captures spatial patterns via a self-attention mechanism, and enables scalable application via a ripple walk sampler strategy. Through comprehensive experiments on data sets generated by different technologies, we show that PAST can effectively characterize spatial domains and facilitate various downstream analyses, including ST visualization, spatial trajectory inference and pseudotime analysis. Also, we highlight the advantages of PAST for multislice joint embedding and automatic annotation of spatial domains in newly sequenced ST data. Compared with existing methods, PAST is the first ST method that integrates reference data to analyze ST data. We anticipate that PAST will open up new avenues for researchers to decipher ST data with customized reference data, which expands the applicability of ST technology.
UPDATE IN INTENSIVE CARE MEDICINE: HEMODYNAMIC MONITORIZATION IN THE CRITICAL PATIENT Percutaneous tracheostomy in the ventilated patient (cid:2) Acute Respiratory

The medical indications of tracheostomy comprise the alleviation of upper airway obstruction; the prevention of laryngeal and upper airway damage due to prolonged translaryngeal intubation in patients subjected to prolonged mechanical ventilation; and the facilitation of airway access for the removal of secretions. Since 1985, percutaneous tracheostomy (PT) has gained widespread acceptance as a method for creating a surgical airway in patients requiring long-term mechanical ventilation. Since then, several comparative trials of PT and surgical tracheostomy have been conducted, and new techniques for PT have been developed. The use of percutaneous dilatation techniques under bronchoscopic control is now increasingly popular throughout the world. Tracheostomy should be performed as soon as the need for prolonged intubation is identiﬁed. However a validated model for the prediction of prolonged mechanical ventilation is not available, and the timing of tracheostomy should be individualized. The present review analyzes the state of the art of PT in mechanically ventilated patients --- this being regarded by many as the technique of choice in performing tracheostomy in critically ill patients.
Climatology and trends in some adverse and fair weather conditions in Canada, 1953–2004

[1] This study characterizes the climatology and trends of some adverse and fair weather occurrence in Canada, on the basis of reliable long-term records of hourly weather and bright sunshine observations at about 90 Canadian stations for the period 1953–2004. The results show that fair or no-weather (i.e., no precipitation or visibility obscuration) trends are generally consistent with the sunshine trends, showing significant increases in southern Canada, with decreases in the Canadian Arctic. The increase of no-weather is most extensive in spring and summer, while the decrease is most extensive in autumn. For the same period, freezing precipitation has become more frequent in the region north of 50°N (especially in spring and autumn) but less frequent in southern British Columbia (BC), central Prairies, and the Great Lakes area in autumn-winter, as well as in northeastern Canada in winter. Blowing snow occurrence has decreased significantly almost everywhere across Canada, with the most significant decline in southwestern Canada in winter. In every season, fog occurrence has significantly increased in the Prairies-Yukon-Northwest Territories and northern BC but decreased in eastern Canada and southern BC. The frequency of low ceiling conditions (<304.8 m, i.e., 1000 feet) has increased in Alberta-BC interior and the Great Lakes area, with the most significant increases in Alberta-BC interior in autumn-winter and in the Great Lakes area in spring; while the other regions have experienced a negative trend, which prevails across the country in summer.
COMPUTATION OF EVAPOTRANSPIRATION IN PARTS OF THE SOUTH PLATTE AND NORTH PLATTE RIVER BASINS USING LANDSAT IMAGERY

It is important to quantify the consumptive water use by the vegetation when managing regional water resources in irrigated areas. Suitable models and algorithms applied to high resolution (30 m) satellite imagery provide a cost effective and time efficient method to obtain evapotranspiration estimations from bare soil and vegetation. The METRIC image processing model calculates net radiation, soil heat flux and sensible heat flux through a number of steps before estimating evapotranspiration as the residual from the energy balance. Sensible heat flux algorithms are calibrated using an operator selected wet and dry pixel. The complete energy balance obtained from the satellite images is calibrated using ground based reference evapotranspiration estimations. The paper describes an application of the METRIC model on parts of the South Platte and North Platte river basins in Colorado and Nebraska for individual days in 1997, 2001 and 2002. Landsat 5 and Landsat 7 shortwave and longwave bands were used. Weather data from selected meteorological stations within the study area was screened and used to estimate reference evapotranspiration. A water balance model was used to estimate evaporation from the soil. During the image processing it was necessary to iterate the selection of the wet and dry pixels after reviewing evapotranspiration behavior for natural vegetation and wet fields at full cover. Uneven distribution of recent precipitation events and operator dependency needed to be addressed. The resulting evapotranspiration maps appear to be congruent with ET from previous studies and will be used by local water management entities.
Gabapentin and oral antidepressants for chronic pruritus: a prospective cohort study evaluating efficacy and side effects in daily dermatological practice

Abstract Background Chronic pruritus is frequently seen in daily dermatological practice and is associated with marked impact on quality of life. Research on the use of gabapentin and oral antidepressants in daily dermatological practice is scarce. Objective To evaluate the efficacy and safety of gabapentin and oral antidepressants in patients with chronic pruritus in daily clinical practice. Methods A prospective observational single-center cohort study was conducted including adult patients with chronic pruritus and an indication for systemic treatment between June 2016 and May 2019. Results Systemic treatment with gabapentin and/or antidepressants was initiated in 31 patients with severe chronic pruritus (median average pruritus NRS score 7.0), in which most cases no underlying origin was identified (83.9%). In patients treated with gabapentin 900–1800 mg/day (N = 25), median average pruritus NRS decreased to 5.5 (IQR 3.0) after 4 weeks and remained stable up to 24 weeks of treatment. Efficacy of antidepressants was variable, with the highest response after initiation of amitriptyline, nortriptyline, and mirtazapine. Side effects were frequently observed in both gabapentin and antidepressant treatments; however, were mostly mild and temporary. Limitations This was a single-site observational study, with limited sample size. Conclusion Treatment with gabapentin and antidepressants should be considered in patients with chronic pruritus unresponsive to conventional treatment.
Giant radiating mafic dyke swarm of the Emeishan Large Igneous Province: Identifying the mantle plume centre

In many continental large igneous provinces, giant radiating dyke swarms are typically interpreted to result from the arrival of a mantle plume at the base of the lithosphere. Mafic dyke swarms in the Emeishan large igneous province (ELIP) have not received much attention prior to this study. We show that the geochemical characteristics and geochronological data of the mafic dykes are broadly similar to those of the spatially associated lavas, suggesting they were derived from a common parental magma. Based on the regional geological data and our field observations, we mapped the spatial distribution patterns of mafic dyke swarms in the ELIP, and recognized six dyke sub‐swarms, forming an overall radiating dyke swarm and converging in the Yongren area, Yunnan province. This location coincides with the maximum pre‐eruptive domal uplift, and is close to the locations of high‐temperature picrites. Our study suggests that the Yongren area may represent the mantle plume centre during the peak of Emeishan magmatism.
Structural insights into the inhibitory mechanism of angiotensin‐I‐converting enzyme by the lactotripeptides IPP and VPP

Human somatic angiotensin‐1‐converting enzyme (sACE) is composed of a catalytic N‐(nACE) and C‐domain (cACE) of similar size with different substrate specificities. It is involved in the regulation of blood pressure by converting angiotensin I to the vasoconstrictor angiotensin II and has been a major focus in the development of therapeutics for hypertension. Bioactive peptides from various sources, including milk, have been identified as natural ACE inhibitors. We report the structural basis for the role of two lacototripeptides, Val‐Pro‐Pro and Ile‐Pro‐Pro, in domain‐specific inhibition of ACE using X‐ray crystallography and kinetic analysis. The lactotripeptides have preference for nACE due to altered polar interactions distal to the catalytic zinc ion. Elucidating the mechanism of binding and domain selectivity of these peptides also provides important insights into the functional roles of ACE.
Can herbicides of different mode of action cause injury symptoms in non-herbicide-tolerant young soybean due to simulated drift?

Abstract Accidental herbicide drift onto neighboring crops, such as soybeans, can seriously harm non-target plants, affecting their growth and productivity. This study examined the impact of simulated drift from ten different herbicides (2,4-D, dicamba, glyphosate, saflufenacil, oxyfluorfen, hexazinone, diuron, diquat, nicosulfuron, and isoxaflutole) on young soybean plants. These herbicides were applied at three simulated drift levels (1/4, 1/16, and 1/32) equivalent to recommended commercial doses, and the resulting symptoms were carefully evaluated. Simulated drift caused distinctive symptoms, including chlorosis, twisting, necrosis, and growth abnormalities, varying depending on each herbicide’s mode of action. Dicamba proved more toxic than 2,4-D, and symptom severity increased with drift proportion, with all herbicides causing over 30% injury at the 1/16 proportion. Notably, 2,4-D, dicamba, glyphosate, hexazinone, and diquat exceeded the half-maximal inhibitory concentration (IC50) value, significantly reducing total biomass. Dicamba consistently caused 50% injury at all proportions, while hexazinone, at the highest dose proportion, led to plant mortality. Dicamba also had biomass accumulation beyond the growth reduction (GR50), whereas hexazinone exhibited less than 10% accumulation due to its capacity to induce plant mortality. This study emphasizes the importance of understanding herbicide drift effects on non-target crops for more effective and safe weed management strategies.
Effect of coating with combined chitosan and gallic acid on shelf-life stability of Jeju black cattle beef

Objective Beef of Jeju black cattle (JBC) is considered as a healthy meat type due to its significantly higher unsaturated fatty acids (UFA). Lipid (e.g., UFA) is highly susceptible to oxidizing agents, which results in the quality deterioration and economic value loss of meat products. Therefore, development and application of novel preservative techniques is necessary to improve the shelf-life stability of high-UFA beef. The objective of this study was to assess the applicability of chitosan-based coatings in preservation of JBC beef. Methods Different coating solutions: 2% chitosan alone, and 2% chitosan containing 0.1% or 0.3% gallic acid were prepared to investigate their applicability in preservation of fresh beef during storage. Jeju black cattle beef (2-cm thick steaks) were non-coated (control) or coated with the above coating solutions, placed on trays, over-wrapped with plastic film and stored at 4°C. The microbiological indices, color, total volatile basic nitrogen (TVBN) and lipid oxidation of the beef were investigated after 1, 10, and 21 days of storage. Results Coating with 2% chitosan alone reduced the spoilage bacteria count, TVBN and thiobarbituric acid reactive substances levels in the beef compared with control during storage (p<0.05). Noticeably, coating with 2% chitosan containing 0.1% or 0.3% gallic acid was more effective on retardation of spoilage bacteria growth, lipid oxidation and discoloration in the beef compared to the chitosan coating alone over the storage period (21 days) (p<0.05). Conclusion Taken together, the combined chitosan and gallic acid coating could be used as a bio-preservative technique in the meat industry.
Identification of host dependency factors involved in SARS-CoV-2 replication organelle formation through proteomics and ultrastructural analysis

ABSTRACT Positive-strand RNA viruses subvert the cellular endomembrane system for the generation of distinct compartments termed replication organelles (ROs) that harbor the site where viral RNAs are generated. In this study, we corroborate that the SARS-CoV-2 non-structural proteins 3 and 4 (nsp3 and nsp4) suffice to remodel the endoplasmic reticulum to form double-membrane vesicles similar to ROs observed in viral infection. Cellular membrane alterations induced by nsp3/4 expression were evaluated through electron tomography and confocal microscopy, and nsp3/4-associated host factors were identified using mass spectrometry. The role of these host factors in virus infection was determined using gene silencing, identifying several host proteins involved in the SARS-CoV-2 replication cycle. Combining the gene silencing approach with ultrastructural analysis of nsp3/4-expressing cells, we found that the host dependency factors FAM149B1, CCAR2, and ZC3HAV1 play a role in the formation of double-membrane vesicles in a replication-independent manner. IMPORTANCE Remodeling of the cellular endomembrane system by viruses allows for efficient and coordinated replication of the viral genome in distinct subcellular compartments termed replication organelles. As a critical step in the viral life cycle, replication organelle formation is an attractive target for therapeutic intervention, but factors central to this process are only partially understood. In this study, we corroborate that two viral proteins, nsp3 and nsp4, are the major drivers of membrane remodeling in SARS-CoV-2 infection. We further report a number of host cell factors interacting with these viral proteins and supporting the viral replication cycle, some of them by contributing to the formation of the SARS-CoV-2 replication organelle. Remodeling of the cellular endomembrane system by viruses allows for efficient and coordinated replication of the viral genome in distinct subcellular compartments termed replication organelles. As a critical step in the viral life cycle, replication organelle formation is an attractive target for therapeutic intervention, but factors central to this process are only partially understood. In this study, we corroborate that two viral proteins, nsp3 and nsp4, are the major drivers of membrane remodeling in SARS-CoV-2 infection. We further report a number of host cell factors interacting with these viral proteins and supporting the viral replication cycle, some of them by contributing to the formation of the SARS-CoV-2 replication organelle.
Contributions from the Second and Third Internal Gravity Modes for the Vertical Motion Response

In an earlier paper of a series of real data integrations of the National Center for Atmospheric Research Community Climate Model (the set of diabatic hidrodynamics nonlinear primitive equations over a sphere has inside gravity-inertia and Rossby modes that can be separated) with tropical heat anomalies display regions of pronounced subsidence and drying surrounding the anomaly located, several thousand kilometers weastward poleward of the heating for cases of tropical Atlantic heating and tropical east Pacific heating. This highly predictable sinking response is established within the first five days of these integrations. The normal-modes decomposition use a set of adiabatic primitive equations linearized about a basic state at rest. The solutions of these equations are separable into horizontal and vertical structure functions and they form identical system with the shallow-water equations. The solutions of the equations with this system show the existence of external and internal vertical modes and are used to partition into Kelvin, gravity, Rossby and mixed Rossby-gravity modes. The most important contribution for the vertical motion response comes from the gravity modes added for all vertical modes Buchmann et al. (1995a). The principal emphasis is given upon the contributions of the second and third internal vertical modes (with equivalent depths on the order of a fews hundred meters) for the vertical motion response.
Selection criteria in the era of perfect competition for drug-eluting stents - a survey of interventional cardiologists in Japan: the selection-DES study

ABSTRACT Background More than 20 years have passed since the first company introduced drug-eluting stent (DES) in 2002, but competing companies still have improved their DESs under regulatory approval. This study aimed to investigate the criteria for interventional cardiologists performing percutaneous coronary intervention (PCI) in selecting a DES. Research design and methods From 10 April 2023, to 30 April 2023, 3,422 cardiologists were requested to complete a questionnaire, of whom 126 responded to the survey. Results Overall, 86.5% of the respondents used Xience cobalt-chromium everolimus-eluting stent (Xience) in > 10% of PCI procedures. For Xience, brand loyalty and calcified lesions were important independent variables for the DES selection criteria. Ultimaster sirolimus-eluting stent (Ultimaster) was not affected by the clinical data delivered by the company, whereas the respondents were shown to seek support for their activities from the Ultimaster supplier. The relationship with the company and/or sales representative and the planned surgical procedure affected the use of Coroflex ISAR NEO sirolimus-eluting polymer-free stent. Conclusions Patient background and lesion characteristics had little impact on the DES selection criteria, suggesting that DES performance has already reached its physical limitations to the extent that respondents may not value further improvements in performance or characteristics of DES.
Participant Satisfaction in a Cardiovascular Disease Prevention Intervention for Midlife Black Women

Background: Midlife Black women suffer disproportionately from cardiovascular disease and are 65% more likely to die following a cardiac event compared with White women. Recruitment and retention of midlife Black women in clinical trials has been historically low. The culturally tailored Midlife Black Women’s Stress Reduction and Wellness (B-SWELL) intervention was codeveloped with the community and designed to lower cardiovascular disease risk in midlife Black women. Objectives: We sought to assess participant satisfaction in the randomized feasibility trial of the B-SWELL intervention. Methods: A feasibility trial comparing the B-SWELL to a wellness intervention was conducted in the winter and spring of 2021 in compliance with pandemic research protocols. An adapted survey tool was used to rate satisfaction with the intervention and its technology using a Likert-type scale (1 [strongly disagree] to 5 [strongly agree]). Survey subscales assessed usefulness, ease, and acceptability of the intervention(s). Results: Randomization yielded no statistical demographic differences (N = 48). Satisfaction for the interventions was high in both the B-SWELL and Wellness intervention groups with mean scores of 4.57 and 4.56, respectively. Mean scores for technology were 4.49 for the B-SWELL and 4.47 for the Wellness group. Subscales were also rated highly. Narrative responses were positively aligned with satisfaction scores. Conclusions: Results support use of cultural adaptation and community participatory methods to develop and deliver interventions targeted to at-risk populations. Culturally adapted interventions designed in collaboration with the community have greater authenticity, increasing the potential for higher recruitment, retention, and participant satisfaction of underrepresented populations. The trial is registered in ClinicalTrials.gov (NCT 04404478).
γ And β Band Oscillation in Working Memory Given Sequential or Concurrent Multiple Items: A Spiking Network Model

Visual Abstract Working memory (WM) can maintain sequential and concurrent information, and the load enhances the γ band oscillation during the delay period. To provide a unified account for these phenomena in working memory, we investigated a continuous network model consisting of pyramidal cells, high-threshold fast-spiking interneurons (FS), and low-threshold nonfast-spiking interneurons (nFS) for working memory of sequential and concurrent directional cues. Our model exhibits the γ (30–100 Hz) and β (10–30 Hz) band oscillation during the retention of both concurrent cues and sequential cues. We found that the β oscillation results from the interaction between pyramidal cells and nFS, whereas the γ oscillation emerges from the interaction between pyramidal cells and FS because of the strong excitation elicited by cue presentation, shedding light on the mechanism underlying the enhancement of γ power in many cognitive executions.
Playing to the Gallery : Corporate Policies and Equity Research Analysts

It is well known that equity analysts choose to cover firms about which they have favorable views. We exploit this fact and use analysts’ coverage decisions to infer their preferences for corporate policies. Next, we show that firms cater to analysts’ preferences. Firms exogenously losing analyst coverage subsequently change their corporate policies away from the preferences of the analyst that drops coverage. Our findings suggest that analysts affect corporate policies. The effects are economically significant and are bigger for small firms and firms with low analyst coverage. Our evidence is consistent with firms altering their corporate policies to cater to the preferences – whether based on beliefs or skills – of equity research analysts.
An unsupervised change detection and recognition system for forestry

Abstract This article presents a new unsupervised method (AutoChange) for change detection and identification. It uses, as an input, two images, acquired on different dates, and a parameter list given by the user. Change detection and identification are performed in separate procedures, and the output is a five channel image estimating the change magnitude and characterizing the changed and unchanged areas. The method carries out the change analysis using homogeneous units selected from the images and only in the ultimate phase the whole image is classified. Changes are detected and identified using clustering in two phases. First, clustering is performed on the earlier and later images to form the so called 'primary clusters'. Second, clustering is performed within the primary clusters of the later image to produce the 'secondary clusters'. Then the change magnitude and change type are obtained by comparing the primary clusters in the earlier image to the secondary clusters in the later image. The method.