Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of New Microneme Proteins in Cryptosporidium parvum and Implication of the Roles of a Rhomboid Membrane Protein (CpROM1) in Host–Parasite Interaction

Apicomplexan parasites possess several unique secretory organelles, including rhoptries, micronemes, and dense granules, which play critical roles in the invasion of host cells. The molecular content of these organelles and their biological roles have been well-studied in Toxoplasma and Plasmodium, but are underappreciated in Cryptosporidium, which contains many parasites of medical and veterinary importance. Only four proteins have previously been identified or proposed to be located in micronemes, one of which, GP900, was confirmed using immunogold electron microscopy (IEM) to be present in the micronemes of intracellular merozoites. Here, we report on the discovery of four new microneme proteins (MICs) in the sporozoites of the zoonotic species C. parvum, identified using immunofluorescence assay (IFA). These proteins are encoded by cgd3_980, cgd1_3550, cgd1_3680, and cgd2_1590. The presence of the protein encoded by cgd3_980 in sporozoite micronemes was further confirmed using IEM. Cgd3_980 encodes one of the three C. parvum rhomboid peptidases (ROMs) and is, thus, designated CpROM1. IEM also confirmed the presence of CpROM1 in the micronemes of intracellular merozoites, parasitophorous vacuole membranes (PVM), and feeder organelles (FO). CpROM1 was enriched in the pellicles and concentrated at the host cell–parasite interface during the invasion of sporozoites and its subsequent transformation into trophozoites. CpROM1 transcript levels were also higher in oocysts and excysted sporozoites than in the intracellular parasite stages. These observations indicate that CpROM1, an intramembrane peptidase with membrane proteolytic activity, is involved in host–parasite interactions, including invasion and proteostasis of PVM and FO.
Opinion: Methodological Shortcomings in the Study on a Prophage-based PCR Test for Lyme Borreliosis

1 Radboudumc, Department of Internal Medicine, Radboudumc Center for Infectious Diseases and Radboud Institute of Health Sciences, Nijmegen, Netherlands, Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands, 3 Epidemiology and Data Science, Amsterdam Public Health, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands, German National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany, 5 ESCMID Study Group for Lyme Borreliosis, Basel, Switzerland
Polymorphonuclear Cells Show Features of Dysfunctional Activation During Fatal Sepsis

Sepsis and septic shock remain leading causes of morbidity and mortality for patients in the intensive care unit. During the early phase, immune cells produce various cytokines leading to prompt activation of the immune system. Polymorphonuclear leukocytes (PMNs) respond to different signals producing inflammatory factors and executing their antimicrobial mechanisms, resulting in the engulfment and elimination of invading pathogens. However, excessive activation caused by various inflammatory signals produced during sepsis progression can lead to the alteration of PMN signaling and subsequent defects in their functionality. Here, we analyzed samples from 34 patients in septic shock, focusing on PMNs gene expression and proteome changes associated with septic shock. We revealed that, compared to those patients who survived longer than five days, PMNs from patients who had fulminant sepsis were characterized by a dysfunctional hyper-activation, show altered metabolism, and recent exit from the cell cycle and signs of cellular lifespan. We believe that this multi-omics approach, although limited, pinpoints the alterations in PMNs’ functionality, which may be rescued by targeted treatments.
Graphene-Based Assemblies for Moist-Electric Generation

Moisture is a ubiquitous and clean resource in nature, which continuously diffuses in the atmosphere and demonstrates huge chemical potential energy that is difficult to be utilized. Recently, the generation of power from interactions between graphene and gaseous water molecules in moisture has triggered great research interest that could provide a novel energy conversion system for our society. graphene-based assemblies have been considered as ideal platforms for moist-electric generation (MEG) in many studies, because of the abundant of functional groups, controllable microstructure and diverse macro morphologies. Therefore, in this short review, we will first state the preparation techniques of graphene-based assemblies for MEG. Then, the fundamental mechanisms of MEG are discussed and the latest advances on graphene MEG are reviewed. Finally, an overview of the current challenges and future development trends in graphene MEG is provided.
Exposure Optimization Trial for Patients With Medical Implants During MRI Exposure: Balance Between the Completeness and Efficiency

Elongated conductors, such as pacemaker leads, can couple to the MRI radio-frequency (RF) field during MRI scan and cause dangerous tissue heating. By selecting proper RF exposure conditions, the RF-induced power deposition can be suppressed. As the RF-induced power deposition is a complex function of multiple clinical factors, the problem remains how to perform the exposure selection in a comprehensive and efficient way. The purpose of this work is to demonstrate an exposure optimization trail that allows a comprehensive optimization in an efficient and traceable manner. The proposed workflow is demonstrated with a generic 40 cm long cardio pacemaker, major components of the clinical factors are decoupled from the redundant data set using principle component analysis, the optimized exposure condition can not only reduce the in vivo power deposition but also maintain good image quality.
SINGLE-ELEMENT-CONTROLLED SINUSOIDAL OSCILLATORS USING CCIIS

Four new single-element-controlled sinusoidal oscillator circuit using two secondgeneration current conveyors (CCIIs), two capacitors and two resistors are presented. Half of the proposed circuits have the advantage of using grounded capacitors. All proposed circuits enjoy oscillation control through a single grounded passive element(s) and independent frequency control through another single passive element(s).
Statistical Machine Learning Model for Uncertainty Planning of Distributed Renewable Energy Sources in Distribution Networks

New energy power systems with high-permeability photovoltaic and wind power are high-dimensional dynamic large-scale systems with nonlinear, uncertain and complex operating characteristics. The uncertainty of new energies creates challenges in detailed analyses of operating conditions and the efficient planning of distribution networks. Probabilistic power flows (PPFs) are effective tools for uncertainty analyses of distribution networks, and they can be applied in stochastic programming, risk assessment and other fields. We propose different forms of PPFs, which are origin moments rather than means and variances, based on point estimation. We design a stochastic programming model suitable for new energy planning in practice, and the PPF results can be used to improve energy stochastic programming methods by considering the principle of maximum entropy (POME) and quadratic fourth-order moment (QFM) estimation. The origin moments of PPFs are transformed into central moments as inputs of QFM based on probability theory. QFM can efficiently estimate the constraint probability levels of stochastic optimal planning models, and the proposed method is verified based on an IEEE 33-node distribution network.
Microbial Growth and Organic Matter Cycling in the Pacific Ocean Along a Latitudinal Transect Between Subarctic and Subantarctic Waters

The Pacific Ocean constitutes about half of the global oceans and thus microbial processes in this ocean have a large impact on global elemental cycles. Despite several intensely studied regions large areas are still greatly understudied regarding microbial activities, organic matter cycling and biogeography. Refined information about these features is most important to better understand the significance of this ocean for global biogeochemical and elemental cycles. Therefore we investigated a suite of microbial and geochemical variables along a transect from the subantarctic to the subarctic Pacific in the upper 200 m of the water column. The aim was to quantify rates of organic matter processing, identify potential controlling factors and prokaryotic key players. The assessed variables included abundance of heterotrophic prokaryotes and cyanobacteria, heterotrophic prokaryotic production (HPP), turnover rate constants of amino acids, glucose, and acetate, leucine aminopeptidase and β-glucosidase activities, and the composition of the bacterial community by fluorescence in situ hybridization (FISH). The additional quantification of nitrate, dissolved amino acids and carbohydrates, chlorophyll a, particulate organic carbon and nitrogen (POC, PON) provided a rich environmental context. The oligotrophic gyres exhibited the lowest prokaryotic abundances, rates of HPP and substrate turnover. Low nucleic acid prokaryotes dominated in these gyres, whereas in temperate and subpolar regions further north and south, high nucleic acid prokaryotes dominated. Turnover rate constants of glucose and acetate, as well as leucine aminopeptidase activity, increased from (sub)tropical toward the subpolar regions. In contrast, HPP and bulk growth rates were highest near the equatorial upwelling and lowest in the central gyres and subpolar regions. The SAR11 clade, the Roseobacter group and Flavobacteria constituted the majority of the prokaryotic communities. Vertical profiles of the biogeochemical and microbial variables markedly differed among the different regions and showed close covariations of the microbial variables and chlorophyll a, POC and PON. The results show that hydrographic, microbial, and biogeochemical properties exhibited distinct patterns reflecting the biogeographic provinces along the transect. The microbial variables assessed contribute to a better and refined understanding of the scales of microbial organic matter processing in large areas of the epipelagic Pacific beyond its well-studied regions.
TELERA—Asynchronous TELEmedicine for Patients With Rheumatoid Arthritis: Study Protocol for a Prospective, Multi-Center, Randomized Controlled Trial

Innovative strategies are needed to adequately assess and monitor disease activity of patients with rheumatoid arthritis (RA) in times of scarce appointments. The aim of the TELERA study is to evaluate the feasibility and performance of asynchronous telemedicine visits based on patient-generated data and patient's drug history. RA patients use a medical app, ABATON, that captures the results of a self-performed quick CRP-test, joint-count, and electronic patient-reported outcomes in between visits. This is a prospective, multi-center, randomized controlled trial performed in four German university centers. The estimated sample size is 120 patients. The main outcome is the agreement of rheumatologists' treatment decisions based on asynchronous telemedicine patient-generated data with traditional in-person rheumatology clinic-based decisions and with patient suggestions. The TELERA trial will provide evidence regarding the implementation of remote care in rheumatology. Clinical Trial Registration: This clinical trial was registered at German Registry for Clinical Trials (DRKS). http://www.drks. de/DRKS00016350, identifier: DRKS00024928.
Application of Zinc and Iron-Based Fertilizers Improves the Growth Attributes, Productivity, and Grain Quality of Two Wheat (Triticum aestivum) Cultivars

Field-based experiments were conducted during wheat cultivation seasons of 2017–2018 and 2018–2019 to minimize the impact of hidden hunger (micronutrient deficiencies) through agronomic biofortification of two wheat cultivars with zinc and iron. Two spring-planted bread wheat cultivars: Zincol-16 (Zn-efficient) and Anaj-17 (Zn-inefficient with high-yield potential) were treated with either zinc (10 kg/ha), iron (12 kg/ha), or their combination to study their effect on some growth attributes (plant height, tillers, and spike length, etc.,), productivity, and quality. No application of zinc and iron or their combinations served as the control. Maximum Zn and Fe contents of grains were improved by sole application of Zn and Fe, respectively. A higher concentration of Ca in grains was observed by the combined application of Zn and Fe. Starch contents were found maximum by sole application of Fe. Sole or combined application of Zn and Fe reduced wet gluten contents. Maximum proteins were recorded in Anaj-17 under control treatments. Zincol-16 produced maximum ionic concentration, starch contents, and wet gluten as compared to Anaj-17. Yield and growth attributes were also significantly (p < 0.05) improved by combined application as compared to the sole application of Zn or Fe. The combined application also produced the highest biological and grain yield with a maximum harvest index. Cultivar Anaj-17 was found more responsive regarding growth and yield attributes comparatively. The findings of the present study showed that the combined application of Zn and Fe produced good quality grains (more Zn, Fe, Ca, starch, and less gluten concentrations) with a maximum productivity of bread wheat cultivars.
Glycogenes in Oncofetal Chondroitin Sulfate Biosynthesis are Differently Expressed and Correlated With Immune Response in Placenta and Colorectal Cancer

Oncofetal chondroitin sulfate expression plays an important role in the development of tumors and the pathogenesis of malaria in pregnancy. However, the biosynthesis and functions of these chondroitin sulfates, particularly the tissue-specific regulation either in tumors or placenta, have not been fully elucidated. Here, by examining the glycogenes availability in chondroitin sulfate biosynthesis such as xylosytransferase, chondroitin synthase, sulfotransferase, and epimerase, the conserved or differential CS glycosylation in normal, colorectal cancer (CRC), and placenta tissue were predicted. We found that the expression of seven chondroitin sulfate biosynthetic enzymes, namely B4GALT7, B3GALT6, B3GAT3, CHSY3, CHSY1, CHPF, and CHPF2, were significantly increased, while four other enzymes (XYLT1, CHST7, CHST15, and UST) were decreased in the colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ) patients. In the human placenta, where the distinct chondroitin sulfate is specifically bound with VAR2CSA on Plasmodium parasite-infected RBC, eight chondroitin sulfate biosynthesis enzymes (CSGALNACT1, CSGALNACT2, CHSY3, CHSY1, CHPF, DSE, CHST11, and CHST3) were significantly higher than the normal colon tissue. The similarly up-regulated chondroitin synthases (CHSY1, CHSY3, and CHPF) in both cancer tissue and human placenta indicate an important role of the proteoglycan CS chains length for Plasmodium falciparum VAR2CSA protein binding. Interestingly, twelve highly expressed chondroitin sulfate enzymes were significantly correlated to worse outcomes (prognosis) in both COAD and READ. Furthermore, we showed that the levels of chondroitin sulfate enzymes are significantly correlated with the expression of immuno-regulators and immune infiltration levels in CRCs and placenta, and involved in multiple essential pathways, such as extracellular matrix organization, epithelial-mesenchymal transition, and cell adhesion. Our study provides novel insights into the oncofetal chondroitin sulfate biosynthesis regulation and identifies promising targets and biomarkers of immunotherapy for CRC and malaria in pregnancy.
Molecular and Immunohistochemical Expression of LTA4H and FXR1 in Canine Oral Melanoma

Oral melanoma is a common canine tumor whose prognosis is considered ominous, but poorly predicted by histology alone. In the present study the gene and protein expression of Leukotriene A4 hydrolase (LTA4H) and Fragile-X-mental retardation-related protein1 (FXR1), both reported as related to metastatic potential in different tumors, were investigated in canine oral melanoma. The main aim of the study was to confirm and quantify the presence of LTA4H and FXR1 genes and protein in oral melanomas. A secondary aim was to investigate their association with histologic prognostic criteria (mitotic count, Ki-67 index). Formalin-fixed-paraffin-embedded canine oral melanomas (36) were collected and histopathological evaluation carried out. Immunolabelling for LTA4H and FXR1 and Ki-67 were performed. RT-PCR evaluated LTA4H and FXR1 gene expressions. Histologically, most tumors were epithelioid cell melanomas (19/36) and were amelanotic, mildly or moderately pigmented (5, 12 and 13/36 respectively), only 6 were highly pigmented. Mitotic count ranged 1-106, Ki-67 index ranged 4.5–52.3. Thirty-two (32/32) melanomas immunolabelled for LTA4H and 33/34 for FXR1. RT-PCR values ranged 0.76–5.11 ΔCt for LTA4H and 0.22–6.24 ΔCt for FXR1. Molecular and immunohistochemical expression of both LTA4H and FXR1 did not statically correlate with mitotic count or Ki-67 index. The present study demonstrates LTA4H and FXR1 gene and protein in canine oral melanoma, however their expression is apparently unrelated to histopathologic prognostic criteria. Although LTA4H and FXR1 seem unrelated to tumor behavior, their extensive expression in the present cohort of cases suggest that they may play a role in canine oral melanoma oncogenesis.
Measuring Failures Proneness: Scale Development and Preliminary Validations

Behavioral failures can serve as precursors for accidents. Yet, individual differences in the predisposition to behavioral failures have predominantly been investigated within relatively narrow parameters, with the focus limited to subsets of behaviors or specific domains. A broader perspective might prove useful in illuminating correlations between various forms of accidents. The current research was undertaken as one step toward developing the concept of behavioral failures proneness in its multidimensional aspect. We report the initial stage of the development and validation of the Failures Proneness questionnaire (FP): a brief, multifaceted, self-report scale of common behavioral failures in everyday settings. In a preliminary phase we conceived an extensive pool of prospective items. Study 1 identified and validated the factor-structure of FP and reduced the scale to a brief measure of 16 items. Study 2 corroborated the factor structure of the FP and evaluated its construct validity by assessing its relationship with the Five Factor Model (FFM) of personality traits. Study 3 tested the criterion-related validity of the FP by assessing its ability to predict deviant behaviors. These studies provide evidence of the FP’s performance in generating valuable information on a broad range of behavioral antecedents of accidents.
Effects of Different Grazing Disturbances on the Plant Diversity and Ecological Functions of Alpine Grassland Ecosystem on the Qinghai-Tibetan Plateau

Grazing is one of the main human disturbance factors in alpine grassland on the Qinghai-Tibet Plateau (QTP), which can directly or indirectly influence the community structures and ecological functions of grassland ecosystems. However, despite extensive field grazing experiments, there is currently no consensus on how different grazing management approaches affect alpine grassland diversity, soil carbon (C), and nitrogen (N). Here, we conducted a meta-analysis of 70 peer-reviewed publications to evaluate the general response of 11 variables related to alpine grassland ecosystems plant diversity and ecological functions to grazing. Overall, the results showed that grazing significantly increased the species richness, Shannon–Wiener index, and Pielou evenness index values by 9.89% (95% CI: 2.75–17.09%), 7.28% (95% CI: 1.68–13.62%), and 3.74% (95% CI: 1.40–6.52%), respectively. Aboveground biomass (AGB) and belowground biomass (BGB) decreased, respectively, by 41.91% (95% CI: −50.91 to −32.88%) and 17.68% (95% CI: −26.94 to −8.52%). Soil organic carbon (SOC), soil total nitrogen (TN), soil C:N ratio, and soil moisture decreased by 13.06% (95% CI: −15.88 to −10.15%), 12.62% (95% CI: −13.35 to −8.61%), 3.27% (95% CI: −4.25 to −2.09%), and 20.75% (95% CI: −27.89 to −13.61%), respectively, whereas, soil bulk density and soil pH increased by 17.46% (95% CI: 11.88–24.53%) and 2.24% (95% CI: 1.01–3.64%), respectively. Specifically, moderate grazing, long-durations (>5 years), and winter grazing contributed to increases in the species richness, Shannon–Wiener index, and Pielou evenness index. However, AGB, BGB, SOC, TN, and soil C:N ratios showed a decrease with enhanced grazing intensity. The response ratio of SOC was positively associated with AGB and BGB but was negatively related to the Shannon–Wiener index and Pielou evenness index. Furthermore, the effects of grazing on plant diversity, AGB, BGB, SOC, and TN in alpine grassland varied with grazing duration, grazing season, livestock type, and grassland type. The findings suggest that grazing should synthesize other appropriate grazing patterns, such as seasonal and rotation grazing, and, furthermore, additional research on grazing management of alpine grassland on the QTP is needed in the future.
LAR Receptor Tyrosine Phosphatase Family in Healthy and Diseased Brain

Protein phosphatases are major regulators of signal transduction and they are involved in key cellular mechanisms such as proliferation, differentiation, and cell survival. Here we focus on one class of protein phosphatases, the type IIA Receptor-type Protein Tyrosine Phosphatases (RPTPs), or LAR-RPTP subfamily. In the last decade, LAR-RPTPs have been demonstrated to have great importance in neurobiology, from neurodevelopment to brain disorders. In vertebrates, the LAR-RPTP subfamily is composed of three members: PTPRF (LAR), PTPRD (PTPδ) and PTPRS (PTPσ), and all participate in several brain functions. In this review we describe the structure and proteolytic processing of the LAR-RPTP subfamily, their alternative splicing and enzymatic regulation. Also, we review the role of the LAR-RPTP subfamily in neural function such as dendrite and axon growth and guidance, synapse formation and differentiation, their participation in synaptic activity, and in brain development, discussing controversial findings and commenting on the most recent studies in the field. Finally, we discuss the clinical outcomes of LAR-RPTP mutations, which are associated with several brain disorders.
Visualizing Phytochemical-Protein Interaction Networks: Momordica charantia and Cancer

The in silico study of medicinal plants is a rapidly growing field. Techniques such as reverse screening and network pharmacology are used to study the complex cellular action of medicinal plants against disease. However, it is difficult to produce a meaningful visualization of phytochemical-protein interactions (PCPIs) in the cell. This study introduces a novel workflow combining various tools to visualize a PCPI network for a medicinal plant against a disease. The five steps are 1) phytochemical compilation, 2) reverse screening, 3) network building, 4) network visualization, and 5) evaluation. The output is a PCPI network that encodes multiple dimensions of information, including subcellular location, phytochemical class, pharmacokinetic data, and prediction probability. As a proof of concept, we built a PCPI network for bitter gourd (Momordica charantia L.) against colorectal cancer. The network and workflow are available at https://yumibriones.github. io/network/. The PCPI network highlights high-confidence interactions for further in vitro or in vivo study. The overall workflow is broadly transferable and can be used to visualize the action of other medicinal plants or small molecules against other diseases.