Miracle-dz/UniFAR-FTUs huggingface dataset:
GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets

Integration of single-cell transcriptome datasets from multiple sources plays an important role in investigating complex biological systems. The key to integration of transcriptome datasets is batch effect removal. Recent methods attempt to apply a contrastive learning strategy to correct batch effects. Despite their encouraging performance, the optimal contrastive learning framework for batch effect removal is still under exploration. We develop an improved contrastive learning-based batch correction framework, GLOBE. GLOBE defines adaptive translation transformations for each cell to guarantee the stability of approximating batch effects. To enhance the consistency of representations alignment, GLOBE utilizes a loss function that is both hardness-aware and consistency-aware to learn batch effect-invariant representations. Moreover, GLOBE computes batch-corrected gene matrix in a transparent approach to support diverse downstream analysis. Benchmarking results on a wide spectrum of datasets show that GLOBE outperforms other state-of-the-art methods in terms of robust batch mixing and superior conservation of biological signals. We further apply GLOBE to integrate two developing mouse neocortex datasets and show GLOBE succeeds in removing batch effects while preserving the contiguous structure of cells in raw data. Finally, a comprehensive study is conducted to validate the effectiveness of GLOBE.
MIB2: metal ion-binding site prediction and modeling server

MOTIVATION MIB2 attempts to overcome the limitation of structure-based prediction approaches, with many proteins lacking a solved structure. MIB2 also offers more accurate prediction performance and more metal ion types. RESULTS MIB2 utilizes both the (PS)2 method and the AlphaFold Protein Structure Database to acquire predicted structures to perform metal ion docking and predict binding residues. MIB2 offers marked improvements over MIB by collecting more metal ion-binding residue templates and using the metal ion type-specific scoring function. It offers a total of 18 types of metal ions for binding site predictions. AVAILABILITY Freely available on the web at http://bioinfo.cmu. edu.tw/MIB2/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Uncommon Mathematical Excursions: Polynomia and Related Realms

Preface Part I. The Province of Polynomia: 1. Horner's foam 2. Polynomial potpourri 3. Polynomial roots and coefficients 4. Solving polynomial equations Part II. Maxministan: 5. Leveling with Lagrange 6. A maxmini miscellany 7. Envelopes and the ladder problem 8. Deflections on an ellipse Part III. The Calculusian Republic: 9. A generalized logarithm for exponential-linear equations 10. Envelopes and asymptotes 11. Derivatives without limits 12. Two calculusian miracles.
Clinical and In Situ Oral Biofilm Formation on Dental Implant Abutment Materials: A Systematic Review.

PURPOSE This review aimed to summarize the current literature on the oral biofilm formation on alternative abutment materials compared with titanium (Ti) or Ti alloy in clinical and in situ conditions. MATERIALS AND METHODS An electronic database search was conducted in PubMed, Cochrane Library, EMBASE, Scopus, Web of Science, LIVIVO, BVS, ProQuest, and OpenGrey up to November 2020. Clinical and in situ studies evaluating the biofilm formed on metallic, ceramic, or polymeric abutment materials compared with Ti or Ti alloy were included. Outcome measures were microbial counts/profile, cell viability, and biofilm coverage/thickness. Clinical parameters were deemed secondary outcomes. Risk of bias was assessed by RoB 2 and ROBINS-I tools. RESULTS A total of 10 clinical and 9 in situ studies were included. Meta-analysis was not performed due to heterogeneity across studies. The abutment materials polytetrafluoroethylene, gold alloy, gold-platinum alloy, cobalt-chromium, alumina, and zirconia were reported. Six out of ten clinical studies (60%) and four out of nine in situ studies (44%) found no qualitative or quantitative microbiologic differences between tested materials. When significant differences were detected, conflicting results were reported. Clinical outcomes were consistent with healthy conditions for all investigated materials. CONCLUSION There is not enough evidence to support the existence of relevant microbiologic differences in the biofilm formed on alternative abutment materials over Ti and its alloys in oral conditions. No evident relationship between microbiologic results and clinical outcomes were found. In situ studies and polymicrobial analyses showed a higher tendency to find significant differences between materials.
Evidence of transmission of influenza A and influenza B co-infection in healthcare workers.

INTRODUCTION Co-infection of influenza A and B has been reported, especially in outbreak situations, but epidemiological and clinical information is limited. We aimed to investigate an outbreak of influenza among health care workers in which the index case suffered from influenza A and B co-infection. METHODOLOGY We investigated the outbreak setting through the utilization of structural questionnaires, molecular methods, and serological tests. RESULTS Among 13 persons, one index case and five confirmed secondary cases were confirmed. The overall influenza infection rate was 46.2% (6/13), with infection rates for influenza A and B at 38.5% (5/13) and 23.1% (3/13), respectively. Interestingly, one of the secondary cases had influenza A and B co-infection identical to the index case. There was no significant association between vaccination status and influenza infection. CONCLUSIONS This study unveils the demonstration of human-to-human influenza A and B co-infection transmission for the first time. Surveillance systems, combined with epidemiological case investigation comprising molecular diagnosis, should be strengthened for future influenza outbreak preparedness.
Cerebrospinal fluid findings in adult patients with obsessive-compulsive disorder: A retrospective analysis of 54 samples

Abstract Objectives Obsessive-compulsive disorder (OCD) can rarely be associated with immunological aetiologies, most notably in Paediatric Autoimmune Neuropsychiatric Disorder Associated with Streptococcal Infections and possibly in autoimmune encephalitis. As cerebrospinal fluid (CSF) analysis is a sensitive method for assessing neuroinflammation, this retrospective study analysed basic CSF parameters and well-characterised as well as novel neuronal autoantibodies in OCD to screen for signs of autoimmunity. Methods Basic CSF findings of 54 adult OCD patients suspected of an organic aetiology were retrospectively compared to a control group of mentally healthy patients (N = 39) with idiopathic intracranial hypertension. Further subgroup analysis included testing for well-characterised neuronal IgG autoantibodies and tissue-based assays using indirect immunofluorescence to screen for novel brain autoantibodies. Results Elevated protein in the CSF of OCD patients compared to the control group (p = 0.043) was identified. Inflammatory markers (pleocytosis/oligoclonal bands/increased IgG-index) were detected in 7% of all patients with OCD. Well-characterised neuronal autoantibodies were not found in any OCD patient, whereas 6/18 (33%) CSF samples showed binding on mouse brain sections in tissue-based assays (binding to neuropil in the basal ganglia/brainstem, cilia of granule cells, blood vessels, nuclear/perinuclear structures). Conclusions While elevated CSF protein is merely a weak indicator of blood CSF barrier dysfunction, the presence of inflammatory CSF changes and novel brain autoantibodies in CSF may indicate OCD subtypes with inflammatory pathomechanism and supports the hypothesis of a rare “autoimmune OCD” subtype.
銀河鉄道の夜 = The night of the milky way train

１ Ｔｈｅ Ａｆｔｅｒｎｏｏｎ Ｃｌａｓｓ ２ Ｔｈｅ Ｐｒｉｎｔｉｎｇ Ｗｏｒｋｓ ３ Ｈｏｍｅ ４ Ｔｈｅ Ｎｉｇｈｔ ｏｆ ｔｈｅ Ｃｅｎｔａｕｒ Ｆｅｓｔｉｖａｌ ５ Ｔｈｅ Ｐｏｌｅ ｏｎ ｔｈｅ Ｈｉｌｌ ６ Ｍｉｌｋｙ Ｗａｙ Ｓｔａｔｉｏｎ ７ Ｔｈｅ Ｎｏｒｔｈｅｒｎ Ｃｒｏｓｓ ａｎｄ ｔｈｅ Ｐｌｉｏｃｅｎｅ Ｃｏａｓｔ ８ Ｔｈｅ Ｂｉｒｄ‐Ｃａｔｃｈｅｒ ９ Ｇｉｏｖａｎｎｉ’ｓ Ｔｉｃｋｅｔ
COVID-19 vaccination and BA.1 breakthrough infection induce neutralising antibodies which are less efficient against BA.4 and BA.5 Omicron variants, Israel, March to June 2022

This work evaluated neutralising antibody titres against wild type (WT) SARS-CoV-2 and four Omicron variants (BA.1, BA.2, BA.4 and BA.5) in healthcare workers who had breakthrough BA.1 infection. Omicron breakthrough infection in individuals vaccinated three or four times before infection resulted in increased neutralising antibodies against the WT virus. The fourth vaccine dose did not further improve the neutralising efficiency over the third dose against all Omicron variants, especially BA.4 and BA.5. An Omicron-specific vaccine may be indicated.
Optimal Impact Angle Guidance via First-Order Optimization Under Nonconvex Constraints

Most of the optimal guidance problems can be formulated as nonconvex optimization problems, which can be solved indirectly by relaxation, convexification, or linearization. Although these methods are guaranteed to converge to the global optimum of the modified problems, the obtained solution may not guarantee global optimality or even the feasibility of the original nonconvex problems. In this paper, we propose a computational optimal guidance approach that directly handles the nonconvex constraints encountered in formulating the guidance problems. The proposed computational guidance approach alternately solves the least squares problems and projects the solution onto nonconvex feasible sets, which rapidly converges to feasible suboptimal solutions or sometimes to the globally optimal solutions. The proposed algorithm is verified via a series of numerical simulations on impact angle guidance problems under state dependent maneuver vector constraints, and it is demonstrated that the proposed algorithm provides superior guidance performance than conventional techniques.
A Single Dosage of l-Arginine Oral Supplementation Induced Post-Aerobic Exercise Hypotension in Hypertensive Patients

Abstract Lowering of peripheral vascular resistance is one of the primary processes involved in blood pressure decrease. Nitric oxide plays a significant role in this process and the availability of l-arginine is a crucial element in nitric oxide biosynthesis. Oral l-arginine supplementation may therefore be a potentiating element in post-exercise hypotension, mediated by its vasodilator action. Thus, the purpose of this study was to investigate if a single dose of l-arginine oral supplementation might impact the post-aerobic exercise blood pressure responses in treated hypertensive individuals. A double-blind, randomized, placebo-controlled crossover trial was conducted. The sample included male (4) and female (6) subjects [62 ± 10 years]. The participants were randomized to ingest one sachet containing 8 grams of l-arginine or placebo (corn starch) dissolved in water (100 ml). The substances were self-administered 120 min before the experimental or control session. The exercise was conducted on a treadmill and consisted of: a 5 min warm-up (50-65% HRreserve); 40 min of running/walking at 60-70% HRreserve; and a 5 min progressive cooldown. After the exercise sessions, blood pressure was measured every 10 min for 60 min. The l-arginine supplementation arm led to significant post-exercise systolic hypotension (mean post-exercise) in relation to rest period (117 ± 12 vs 125 ± 15 mmHg - p = 0.004 [l-arginine] and 121 ± 11 vs 125 ± 15 - p = 0.341 [placebo]). In addition, a systolic net effect of −6.9 ± 3.6 mmHg [p = 0.046] was identified for the mean post-exercise values. Therefore, this study showed that a single dosage of l-arginine oral supplementation induced post-aerobic exercise hypotension in hypertensive patients.
Deep origin and gradual evolution of transporting tissues: Perspectives from across the land plants

Abstract The evolution of transporting tissues was an important innovation in terrestrial plants that allowed them to adapt to almost all nonaquatic environments. These tissues consist of water-conducting cells and food-conducting cells and bridge plant–soil and plant–air interfaces over long distances. The largest group of land plants, representing about 95% of all known plant species, is associated with morphologically complex transporting tissue in plants with a range of additional traits. Therefore, this entire clade was named tracheophytes, or vascular plants. However, some nonvascular plants possess conductive tissues that closely resemble vascular tissue in their organization, structure, and function. Recent molecular studies also point to a highly conserved toolbox of molecular regulators for transporting tissues. Here, we reflect on the distinguishing features of conductive and vascular tissues and their evolutionary history. Rather than sudden emergence of complex, vascular tissues, plant transporting tissues likely evolved gradually, building on pre-existing developmental mechanisms and genetic components. Improved knowledge of the intimate structure and developmental regulation of transporting tissues across the entire taxonomic breadth of extant plant lineages, combined with more comprehensive documentation of the fossil record of transporting tissues, is required for a full understanding of the evolutionary trajectory of transporting tissues.
Identifying and expression analysis of WD40 transcription factors in walnut

Walnut (Juglans regia L.) is an important woody oil plant and will be affected by abiotic and biological stress during its growth and development. The WD‐repeat (WD40) protein is widely involved in plant growth, development, metabolism, and abiotic stress response. To explore the stress response mechanism of walnut, based on the complete sequencing results of the walnut genome, this study identified and analyzed the physiological, biochemical, genetic structure, and conservative protein motifs of 42 JrWD40 genes, whose expression to abnormal temperature were tested to predict the potential biological function. The results showed that the open reading frame (ORF) of theseWD40 genes were 807–2,460 bp, encoding peptides were 29,610.55–90,387.98 Da covering 268–819 amino acids, as well as 12–112 phosphorylation sites. JrWD40 proteins were highly conserved with four to five WD40 domains and shared certain similarity to WD40 proteins from Arabidopsis thaliana (L.) Heynh. JrWD40 genes can be induced to varying degrees by low and high temperature treatments. JrWD40‐32, JrWD40‐27, JrWD40‐35, and JrWD40‐21 are affected by high temperature more seriously and their expression levels are higher; while JrWD40‐37, JrWD40‐26, JrWD40‐20, JrWD40‐24, and other genes are inhibited under low temperature stress. JrWD40‐40, JrWD40‐28, and JrWD40‐18 were first suppressed with low expression, while as the treatment time prolonging, the expression level was increased under cold condition. JrWD40‐14, JrWD40‐18, JrWD40‐34, and JrWD40‐3 displayed strong transcriptions response to both heat and cold stress. These results indicated that JrWD40 genes can participate in walnut adaptation to adversity and can be used as important candidates for walnut resistance molecular breeding.
Factors associated with poor access to HIV and sexual and reproductive health services in Nigeria for women and girls living with HIV during the COVID-19 pandemic

Aim: To determine the proportion of women and girls living with HIV (WGLHIV) who had poor access to HIV, tuberculosis and sexual and reproductive health (SRH) services in Nigeria during the COVID-19 pandemic and associated factors. Methods: This was a cross-sectional study that recruited WGLHIV with six categories of vulnerability (sex work, transactional sex, injecting or using illegal drugs, people on the move, transgender women and people with a disability) through an online survey conducted in ten Nigerian states between june and October 2021. The associations between the limited access to HIV, tuberculosis and SRH services due to COVID-19, the categories of vulnerability and the financial and non-financial barriers to these services were determined using multivariable logistics regression analysis. Results: Over 6 in 10, almost 2 in 10, and almost 4 in 10 WGLHIV had limited access to HIV, tuberculosis and SRH services respectively during the COVID-19 pandemic. Transgender women had 3.59 (95% CI 2.19–5.91) higher odds, women who engaged in sex work had 4.51 (95% CI 2.28–8.42) higher odds, and women who inject or use illegal drugs had 2.39 (95% CI 1.47–32.90) higher odds of facing limited access to sexual and reproductive health services when it was needed. In addition, the direct consequences of the COVID-19 crisis, such as the closure of HIV services and SRH service points, exacerbated pre-existing barriers significantly. Having no money, having to pay additional unofficial fees and the lack of security on the road to the health facility were the barriers with the greatest impact on access to health services. Conclusions: The COVID-19 pandemic had a negative impact on the access of WGLHIV to essential health services. This impact was disproportionately higher for marginalised groups. WGLHIV need non-discriminatory and affordable access to essential health services during the pandemic.
Isatuximab in the Treatment of Multiple Myeloma: A Review and Comparison With Daratumumab

Multiple myeloma (MM) is a hematologic malignancy characterized by the proliferation of clonal plasma cells. Although advances in treatment have markedly improved survival outcomes for patients with MM, this disease is still considered incurable owing to its high incidence of relapse and refractoriness. Isatuximab is an anti-CD38 monoclonal antibody that can induce apoptosis in myeloma cells through a variety of mechanisms. Many clinical studies have demonstrated the efficacy and efficiency of isatuximab in both relapsed/refractory multiple myeloma (RRMM) and newly diagnosed multiple myeloma, leading to its approval for the treatment of adults with RRMM in combination therapies. In this review, the structure, mechanisms of action, pharmacokinetics, pharmacogenetics, and safety profile of isatuximab in MM are summarized. Additionally, isatuximab is compared with daratumumab in terms of mechanism and efficacy.
Highly efficient pentacene/C60 organic solar cells

We report on highly efficient organic solar cells based on polycrystalline thin films of pentacene, a material that has been widely investigated for p-type transport layers in organic field-effect transistors (OFET). The spectral measurement of external quantum efficiencies (EQE) shows that these high efficiencies are due to the efficient light-harvesting occurring throughout the visible spectrum. In particular, the peak EQE of 69% has been measured at a wavelength of 668 nm where most of the excitons are generated inside the pentacene layer. This suggests that the polycrystalline nature of pentacene films leading to high field-effect mobilities in OFET also results in relatively large exciton diffusion lengths which are desired in multilayer organic solar cells. In an effort to understand these devices, we model the external quantum efficiencies as a function of wavelength based on the exciton diffusion model using the complex indices (n, k) of participating materials. This study provides information on the correlation of optical properties of photoactive materials to the spectral responses and allows one to estimate exciton diffusion lengths. Based on this information, we discuss the optimization of layer structures that can lead to maximization of the photocurrent under standard illumination condition.
In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains

The cilium is an antenna-like organelle that performs numerous cellular functions, including motility, sensing, and signaling. The base of the cilium contains a selective barrier that regulates the entry of large intraflagellar transport (IFT) trains, which carry cargo proteins required for ciliary assembly and maintenance. However, the native architecture of the ciliary base and the process of IFT train assembly remain unresolved. In this work, we used in situ cryo–electron tomography to reveal native structures of the transition zone region and assembling IFT trains at the ciliary base in Chlamydomonas. We combined this direct cellular visualization with ultrastructure expansion microscopy to describe the front-to-back stepwise assembly of IFT trains: IFT-B forms the backbone, onto which bind IFT-A, dynein-1b, and finally kinesin-2 before entry into the cilium. Description Close-up view of transport train assembly Cilia and flagella extend from the cell surface of various eukaryotic cells and perform diverse motility and signaling functions. The base of the cilium controls the entry of large intraflagellar transport trains that carry important cargo proteins throughout this specialized organelle. Defects in the ciliary base result in altered ciliary composition and human diseases. van den Hoek et al. used a combination of cryo–electron tomography and expansion microscopy techniques to study the molecular architecture of the ciliary base in the green alga Chlamydomonas reinhardtii. Their findings elucidate how intraflagellar transport trains assemble before they enter cilia and demonstrate the possibility of visualizing dynamic events with molecular resolution inside native cells. —SMH Native molecular structure of the Chlamydomonas ciliary transition zone and intraflagellar transport chain assembly is described.
Patient‐facing communication for cytopathologists: A framework for disclosing diagnostic error

Medical errors are a major source of harm to patients. Regulatory bodies mandate and patient safety experts advocate the disclosure of medical errors to patients to promote transparency and to create accountability for improving health care processes. Although pathologists regularly report errors—either to pathology or clinical colleagues or via internal safety reporting systems—few pathologists directly disclose those errors to patients. Yet many pathologists are interested in participating in the direct disclosure of medical errors to patients and may even be mandated to do so. When surveyed on why they do not directly disclose errors to patients, pathologists commonly cite a lack of confidence and a lack of training. Another barrier cited is the lack of a preexisting relationship between the pathologist and the patient. With respect to this last barrier, cytopathologists have a distinct advantage over surgical or clinical pathologists, as many cytopathologists regularly interact with and develop a rapport with patients when they are performing fine‐needle aspiration (FNA) procedures. To improve the safety culture in pathology, direct error disclosure practices must be developed, supported, and strengthened. It is critical for cytopathologists to be comfortable with disclosing errors to patients. Being comfortable with disclosing an error, however, requires training, practice, and advance reflection. Using a practical, case‐based format centered around FNA examples, this article addresses how to disclose a medical error to a patient. It provides a framework, heuristic principles, and structured conversation systems and talking points to guide the inexperienced pathologist to find his or her voice in a challenging disclosure conversation.