Miracle-dz/UniFAR-FTUs huggingface dataset:
MGATMDA: Predicting Microbe-Disease Associations via Multi-Component Graph Attention Network

Microbes are parasitic in various human body organs and play significant roles in a wide range of diseases. Identifying microbe-disease associations is conducive to the identification of potential drug targets. Considering the high cost and risk of biological experiments, developing computational approaches to explore the relationship between microbes and diseases is an alternative choice. However, most existing methods are based on unreliable or noisy similarity, and the prediction accuracy could be affected. Besides, it is still a great challenge for most previous methods to make predictions for the large-scale dataset. In this work, we develop a multi-component Graph Attention Network (GAT) based framework, termed MGATMDA, for predicting microbe-disease associations. MGATMDA is built on a bipartite graph of microbes and diseases. It contains three essential parts: decomposer, combiner, and predictor. The decomposer first decomposes the edges in the bipartite graph to identify the latent components by node-level attention mechanism. The combiner then recombines these latent components automatically to obtain unified embedding for prediction by component-level attention mechanism. Finally, a fully connected network is used to predict unknown microbes-disease associations. Experimental results showed that our proposed method outperformed eight state-of-the-art methods. Case studies for two common diseases further demonstrated the effectiveness of MGATMDA in predicting potential microbe-disease associations. The codes are available at Github https://github.com/dayunliu/MGATMDA.
Synthesis of vertically aligned wafer-scale tantalum disulfide using high-Ar/H2S ratio plasma

Nanostructural modification of two-dimensional (2D) materials has attracted significant attention for enhancing hydrogen evolution reaction (HER) activity. In this study, the nanostructure of TaS2 films was controlled by controlling the Ar/H2S gas ratio used in plasma-enhanced chemical vapor deposition (PECVD). At a high Ar/H2S gas ratio, vertically aligned TaS2 (V-TaS2) films were formed over a large-area (4 in) at a temperature of 250 °C, which, to the best of our knowledge, is the lowest temperature reported for PECVD. Furthermore, the plasma species formed in the injected gas at various Ar/H2S gas ratios were analyzed using optical emission spectroscopy to determine the synthesis mechanism. In addition, the 4 in wafer-scale V-TaS2 was analyzed by x-ray photoelectron spectroscopy, transmission electron microscopy, and atomic force microscopy, and the HER performance of the as-synthesized TaS2 fabricated with various Ar/H2S ratios was measured. The results revealed that, depending on the film structure of TaS2, the HER performance can be enhanced owing to its structural advantage. Furthermore, the excellent stability and robustness of V-TaS2 was confirmed by conducting 1000 HER cycles and post-HER material characterization. This study provides important insights into the plasma-assisted nanostructural modification of 2D materials for application as enhanced electrocatalysts.
KD-Box: Line-segment-based KD-tree for Interactive Exploration of Large-scale Time-Series Data

Time-series data–usually presented in the form of lines–plays an important role in many domains such as finance, meteorology, health, and urban informatics. Yet, little has been done to support interactive exploration of large-scale time-series data, which requires a clutter-free visual representation with low-latency interactions. In this paper, we contribute a novel line-segment-based KD-tree method to enable interactive analysis of many time series. Our method enables not only fast queries over time series in selected regions of interest but also a line splatting method for efficient computation of the density field and selection of representative lines. Further, we develop KD-Box, an interactive system that provides rich interactions, e.g., timebox, attribute filtering, and coordinated multiple views. We demonstrate the effectiveness of KD-Box in supporting efficient line query and density field computation through a quantitative comparison and show its usefulness for interactive visual analysis on several real-world datasets.
Factors of Hospitals Associated With an Independent Hospice Care Unit

Few studies have examined why some hospitals operate independent hospice units (IHUs) and others do not. This study aims to investigate the organizational factors of hospitals having IHU. The units of analysis were individual hospitals. The study had a cross-sectional design and used health insurance claims data of 349 hospitals in Korea from January 1 to December 31, 2019. The dependent variable was whether a hospital operated an IHU. The independent variables were the percentage of patients with cancer, overall severity of patients, percentage of patients 60 years and older, health care cost per patient, percentage of inpatients, and nurse staffing level. Independent hospice units were present at 21.2% of the hospitals (74/349). The odds of having an IHU were significantly associated with the following factors: the percentage of patients with cancer (odds ratio [OR], 1.228; 95% confidence interval [CI], 1.071-1.408; P = .003), disease severity (OR, 5.129; 95% CI, 2.477-10.622; P < .001), percentage of patients 60 years and older (OR, 1.053; 95% CI, 1.015-1.092; P = .006), health care cost per patient (OR, 1.018; 95% CI, 1.009-1.027; P < .001), and nurse staffing level (OR, 0.439; 95% CI, 0.292-0.661; P < .001). The organizational factors of hospitals operating IHUs were similar to those of hospice facilities.
The YTHDF proteins ECT2 and ECT3 bind largely overlapping target sets and influence target mRNA abundance, not alternative polyadenylation

Gene regulation via N6-methyladenosine (m6A) in mRNA involves RNA-binding proteins that recognize m6A via a YT521-B homology (YTH) domain. The plant YTH domain proteins ECT2 and ECT3 act genetically redundantly in stimulating cell proliferation during organogenesis, but several fundamental questions regarding their mode of action remain unclear. Here, we use HyperTRIBE (targets of RNA-binding proteins identified by editing) to show that most ECT2 and ECT3 targets overlap, with only a few examples of preferential targeting by either of the two proteins. HyperTRIBE in different mutant backgrounds also provides direct views of redundant, ectopic, and specific target interactions of the two proteins. We also show that contrary to conclusions of previous reports, ECT2 does not accumulate in the nucleus. Accordingly, inactivation of ECT2, ECT3, and their surrogate ECT4 does not change patterns of polyadenylation site choice in ECT2/3 target mRNAs, but does lead to lower steady-state accumulation of target mRNAs. In addition, mRNA and microRNA expression profiles show indications of stress response activation in ect2/ect3/ect4 mutants, likely via indirect effects. Thus, previous suggestions of control of alternative polyadenylation by ECT2 are not supported by evidence, and ECT2 and ECT3 act largely redundantly to regulate target mRNA, including its abundance, in the cytoplasm.
Effects of work conditions and organisational strategies on nurses' mental health during the COVID‐19 pandemic

Abstract Aims This study aims to examine coronavirus disease 2019 (COVID‐19) pandemic‐related work factors for adverse effects on the mental health and whether organisational strategies attenuate these effects. Background COVID‐19 pandemic has led to increased work burden and mental health risks for nurses. Methods A total of 1499 Taiwanese full‐time nurses completed a web‐based questionnaire between July and December 2020. Pandemic‐related work conditions, namely, increased working hours, caring for COVID‐19 patients, occupational stigma and redeployment, were assessed. Organisational strategies to combat pandemic‐related work stressors including compensation to workers and adequate protection equipment were surveyed. Outcome measures were intention to leave, burnout and depression assessed using validated questionnaires. Results Redeployment, increased working hours and occupational stigma were associated with adverse mental health and intention to leave in logistic regression analysis. Caring for COVID‐19 patients was negatively associated with depression. Adequate compensation for workers modified the association between redeployment and burnout. Conclusions Pandemic‐related work conditions were associated with adverse mental health and intention to leave. Organisational strategies attenuated the adverse impact of the pandemic. Implications for Nursing Management Efforts to decrease stigma and organisational strategies including compensation for workers and adequate protection equipment provision should be adopted to improve nurses' health during a pandemic.
Joint t-SNE for Comparable Projections of Multiple High-Dimensional Datasets

We present Joint t-Stochastic Neighbor Embedding (Joint t-SNE), a technique to generate comparable projections of multiple high-dimensional datasets. Although t-SNE has been widely employed to visualize high-dimensional datasets from various domains, it is limited to projecting a single dataset. When a series of high-dimensional datasets, such as datasets changing over time, is projected independently using t-SNE, misaligned layouts are obtained. Even items with identical features across datasets are projected to different locations, making the technique unsuitable for comparison tasks. To tackle this problem, we introduce edge similarity, which captures the similarities between two adjacent time frames based on the Graphlet Frequency Distribution (GFD). We then integrate a novel loss term into the t-SNE loss function, which we call vector constraints, to preserve the vectors between projected points across the projections, allowing these points to serve as visual landmarks for direct comparisons between projections. Using synthetic datasets whose ground-truth structures are known, we show that Joint t-SNE outperforms existing techniques, including Dynamic t-SNE, in terms of local coherence error, Kullback-Leibler divergence, and neighborhood preservation. We also showcase a real-world use case to visualize and compare the activation of different layers of a neural network.
Morphology, physiology and synaptic connectivity of local interneurons in the mouse somatosensory thalamus

The thalamic reticular nucleus (TRN) neurons, projecting across the external medullary lamina, have long been considered to be the only significant source of inhibition of the somatosensory ventral posterior (VP) nuclei of the thalamus. Here we report for the first time effective local inhibition and disinhibition in the VP. Inhibitory interneurons were found in GAD67–GFP‐expressing mice and studied using in vitro multiple patch clamp. Inhibitory interneurons have expansive bipolar or tripolar morphologies, reach across most of the VP nucleus and display low threshold bursting behaviour. They form triadic and non‐triadic synaptic connections onto thalamocortical relay neurons and other interneurons, mediating feedforward inhibition and disinhibition. Synaptic inputs arrive before those expected from the TRN neurons, suggesting that local inhibition plays an early and significant role in the functioning of the somatosensory thalamus.
‘Depression is not a familiar word’: A mixed-methods approach to describe the experience of primary care nurses treating depression in rural Guatemala

Background: As the burden of mental health disorders continues to increase worldwide, there is significant need to describe the cultural variations in presentation, diagnosis and treatment of these diseases. An understanding of these variations can lead to the development of more effective programs to manage these conditions. In Guatemala, depression is the second-leading cause of disability and yet mental health treatment resources are scarce, particularly for indigenous individuals. Aims: The primary research aim was to describe primary care nurses’ explanatory models of depression in their clinical work in indigenous communities in Guatemala. A secondary research aim was to describe training and resources which would support and empower these nurses, in order to lessen risk for burnout. Methods: A cross-sectional mixed methods survey was designed to elicit nurses’ perspectives on the presentation, cause and treatment of depression in the communities they serve, as well as their clinical and emotional comfort in working with depressed individuals. Two subsequent focus groups gathered qualitative commentary which informed training and resource recommendations. Theoretical thematic analysis was used to generate codes and themes from focus group transcripts and survey responses. Results: Guatemalan primary care nurses described symptoms of depression in their cultural context, identified socioeconomic factors which contribute to depression in their communities, and detailed treatment preferences. Limited referral options and concern for privacy made connecting patients to mental health care difficult. Nurses emphasized the need for community education on depression and for supplemental mental health resources which would increase their capacity to identify and treat depression. Conclusions: Primary care nurses in Guatemala identify and treat depression despite limited resources. Further investigations should focus on creating training modalities which include front-line nurses, given their critical role in the health system.
LoopGrafter: Visual Support for the Grafting Workflow of Protein Loops

In the process of understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on the exploration of regions in proteins called loops. Analyzing various characteristics of these regions helps the experts to design the transfer of the desired function from one protein to another. This process is denoted as loop grafting. As this process requires extensive manual treatment and currently there is no proper visual support for it, we designed LoopGrafter: a web-based tool that provides experts with visual support through all the loop grafting pipeline steps. The tool is logically divided into several phases, starting with the definition of two input proteins and ending with a set of grafted proteins. Each phase is supported by a specific set of abstracted 2D visual representations of loaded proteins and their loops that are interactively linked with the 3D view onto proteins. By sequentially passing through the individual phases, the user is shaping the list of loops that are potential candidates for loop grafting. In the end, the actual in-silico insertion of the loop candidates from one protein to the other is performed and the results are visually presented to the user. In this way, the fully computational rational design of proteins and their loops results in newly designed protein structures that can be further assembled and tested through in-vitro experiments. LoopGrafter was designed in tight collaboration with protein engineers, and its final appearance reflects many testing iterations. We showcase the contribution of LoopGrafter on a real case scenario and provide the readers with the experts' feedback, confirming the usefulness of our tool.
S-arylation of 2-mercaptobenzazoles: a comprehensive review

ABSTRACT In recent years 2-arylthio-benzazoles (benzothiazoles, benzoxazoles, and benzimidazoles) have attracted more and more attention due to their diverse biological and pharmacological properties. Consequently, great efforts have been devoted to exploiting efficient strategies towards the synthesis of titled compounds. Among the different methods reported for the synthesis of 2-arylthio-benzazoles, the most general and applicable one consists of the C–S cross-coupling of corresponding 2-mercaptobenzazoles with various electrophilic coupling partners. This protocol has advantages of the easily accessible starting materials, satisfactory yield of products, broad substrate scope, and high generality which makes it a useful and attractive method for the construction of various 2-arylthio-benzazoles. In this review, we highlight the significant advances achieved in this field from 1987 to 2017, with special emphasis on the mechanistic aspects of the reactions. GRAPHICAL ABSTRACT
Intracameral sustained release bimatoprost implants (Durysta)

ABSTRACT Background Sustained release drug delivery has the potential to change glaucoma care by decreasing the challenge of medication adherence. Many approaches are in development, but this review focuses on Durysta (Allergan plc, Dublin, Ireland), the only FDA-approved sustained release intracameral treatment available at this time. Key Findings Durysta is a bimatoprost sustained release (BimSR) intracameral implant. Clinical trials have demonstrated that BimSR implants can provide comparable levels of intraocular pressure (IOP) control as topical eyedrops. BimSR has advantages such as decreasing concerns regarding drop adherence, reducing ocular surface and periocular side effects from topical drops, and decreased daily treatment burden for patients. In addition, studies have shown continued IOP lowering in some eyes during extended follow-up periods when all of the BimSR medication has already been delivered. Hypothesized mechanisms to explain this finding include increased matrix metalloproteinase expression that causes extracellular matrix reorganization to permit greater aqueous outflow, as well as decreased episcleral venous pressure. The major safety concern at this time for Durysta and future intracameral implants is corneal endothelial cell loss, which was worse with repeat BimSR administration compared to single dosing. Several studies are underway to investigate mechanisms of action and to better understand safe and effective dosing of medications in this class.
Single in‐line biomass probe detects CHO cell growth by capacitance and bacterial contamination by conductivity in bioreactor

Real time process data facilitates timely decisions, enables better process control, and can increase quality assurance. Biological drugs (mol. Wt. ≥ 40 kDa) are manufactured using mammalian cells such as Chinese hamster ovary (CHO) cells in bioreactors and have significant risks of contamination during processing. In such processes, in‐line monitoring of biomass can provide real‐time cell growth profiles and indications of bioreactor health.
Development of Electrolytes for Single Crystal NMC532/Artificial Graphite Cells with Long Lifetime

NMC532/artiﬁcial graphite cells using single crystal NMC532 active material can have excellent long term lifetime at 4.4 V and elevated temperature if appropriate electrolytes are used. However, electrolytes developed earlier for these cells and reported in the literature cannot support even C/2 rates during charging without unwanted lithium plating at room temperature. This work is thus focused on the development of new electrolytes for single crystal NMC532/artiﬁcial graphite cells that can yield long lifetime and support higher charging rates. Ex-situ and in-situ gas measurements, ultra-high precision coulometry, isothermal microcalorimetry, lithium plating tests and long term cycling tests were used for the screening of electrolytes. Electrolytes with 2% vinylene carbonate (VC) + 1% ethylene sulfate (DTD) additives or 2% ﬂuoroethylene carbonate (FEC) + 1% DTD additives yield single-crystal NMC532/graphite cells with long lifetime that can support C-rate charging at 20 ◦ C. unrestricted in any
Draft Genome Sequence of Leptospira yasudae Strain BJ3, Isolated from the Soil of an Ex Situ Wild Animal Conservation Area

Previously, a novel Leptospira strain (BJ3) was isolated from the soil of an ex situ wild animal conservation area in Perak, Malaysia. Molecular identification via whole-genome sequencing confirmed that the strain was Leptospira yasudae. Here, we report the draft genome sequence of L. yasudae strain BJ3. ABSTRACT Previously, a novel Leptospira strain (BJ3) was isolated from the soil of an ex situ wild animal conservation area in Perak, Malaysia. Molecular identification via whole-genome sequencing confirmed that the strain was Leptospira yasudae. Here, we report the draft genome sequence of L. yasudae strain BJ3.
Survey of Beak and Feather Disease Virus (BFDV) in Guatemalan Neotropical Psittacine Birds

Abstract: Beak and feather disease virus (BFDV), a circovirus, is the etiologic agent of psittacine beak and feather disease (PBFD), a progressive and often fatal disease in Psittaciformes. Even though neotropical psittacine species are more resistant to clinical infection than Old World species, BFDV is recognized as a threat to immunologically naïve wild psittacine flocks and its epidemiologic control is paramount for conservation efforts in Neotropical species. Samples were collected from multiple psittacine species, including Ara species, Amazona species, and the white-crowned parrot (Pionus senilis) from the only rescue center in Guatemala with formal psittacine rehabilitation and reintroduction programs. A total of 117 birds, with 101 adults and 16 juveniles of unknown sex, were tested for BFDV by means of a real-time polymerase chain reaction (PCR) assay. The BFDV prevalence found in this study was 0%, (95% confidence interval, 0%–6.0%). Seven 2–8-year-old scarlet macaws (Ara macao cyanoptera) with positive results from previous surveys by conventional PCR yielded negative results in this study, suggesting complete infection resolution.
Developing Regional Ecological Networks Along the Grand Canal based on an Integrated Analysis Framework

Abstract: As a complex social ecosystem network, the area along the Grand Canal has a prominent contradiction between the demand for economic development and the protection of natural resources, which means that there is an urgent need for ecological restoration and environmental protection. Using ArcGIS, Conefor, Linkage Mapper and other software platforms, this paper developed an integrated analysis framework, through loose coupling of the attribute-function-structure index system and a series of methods such as the least cost path, circuit theory and moving window search. Based on the framework, we resolve a series of scientific issues in developing regional ecological networks, such as the selection of ecological sources, the simulation of potential ecological corridors, the assessment of the importance of ecological sources and corridors, and the identification of key ecological nodes. Moreover, an overall conservation pattern of the regional ecological network is constructed. The results show that: 1) A total of 88 important ecological sources are identified in the study area. The patches with high centrality values are mainly concentrated in the southern mountainous area and the areas with abundant rivers and lakes. 2) A total of 138 important ecological corridors are identified, and they are not evenly distributed. Extremely important corridors mostly appear between important patches, and very important corridors are mainly distributed in the central area. 3) Fifteen ecological pinch points are extracted, and they are mainly concentrated in the northern part of the study area and eastern Zhejiang Province. The barriers are mostly concentrated in the southern and northern parts of the study area. 4) Combining the demands of ecological protection and socioeconomic development, we propose an overall ecological conservation pattern of “one axis, five sections, multiple cores and multiple nodes” to effectively guide future ecological restoration work. These results can provide a useful reference and spatial guidance for decision makers in terms of ecological restoration and cooperation on cross-regional ecological protection along the Grand Canal.