Miracle-dz/UniFAR-FTUs huggingface dataset:
Interleukin-2-Inducible T-Cell Kinase Deficiency Impairs Early Pulmonary Protection Against Mycobacterium tuberculosis Infection

Interleukin-2 (IL-2) inducible T-cell kinase (ITK) is a non-receptor tyrosine kinase highly expressed in T-cell lineages and regulates multiple aspects of T-cell development and function, mainly through its function downstream of the T-cell receptor. Itk deficiency can lead to CD4 lymphopenia and Epstein-Bar virus (EBV)-associated lymphoproliferation and recurrent pulmonary infections in humans. However, the role of the ITK signaling pathway in pulmonary responses in active tuberculosis due to Mtb infection is not known. We show here that human lungs with active tuberculosis exhibit altered T-cell receptor/ITK signaling and that Itk deficiency impaired early protection against Mtb in mice, accompanied by defective development of IL-17A-producing γδ T cells in the lungs. These findings have important implications of human genetics associated with susceptibility to Mtb due to altered immune responses and molecular signals modulating host immunity that controls Mtb activity. Enhancing ITK signaling pathways may be an alternative strategy to target Mtb infection, especially in cases with highly virulent strains in which IL-17A plays an essential protective role.
A Machine Learning and Wearable Sensor Based Approach to Estimate External Knee Flexion and Adduction Moments During Various Locomotion Tasks

Joint moment measurements represent an objective biomechanical parameter of knee joint load in knee osteoarthritis (KOA). Wearable sensors in combination with machine learning techniques may provide solutions to develop assistive devices in KOA patients to improve disease treatment and to minimize risk of non-functional overreaching (e.g., pain). The purpose of this study was to develop an artificial neural network (ANN) that estimates external knee flexion moments (KFM) and external knee adduction moments (KAM) during various locomotion tasks, based on data obtained by two wearable sensors. Thirteen participants were instrumented with two inertial measurement units (IMUs) located on the right thigh and shank. Participants performed six different locomotion tasks consisting of linear motions and motions with a change of direction, while IMU signals as well as full body kinematics and ground reaction forces were synchronously recorded. KFM and KAM were determined using a full body biomechanical model. An ANN was trained to estimate the KFM and KAM time series using the IMU signals as input. Evaluation of the ANN was done using a leave-one-subject-out cross-validation. Concordance of the ANN-estimated KFM and reference data was categorized for five tasks (walking straight, 90° walking turn, moderate running, 90° running turn and 45° cutting maneuver) as strong (r ≥ 0.69, rRMSE ≤ 23.1) and as moderate for fast running (r = 0.65 ± 0.43, rRMSE = 25.5 ± 7.0%). For all locomotion tasks, KAM yielded a lower concordance in comparison to the KFM, ranging from weak (r ≤ 0.21, rRMSE ≥ 33.8%) in cutting and fast running to strong (r = 0.71 ± 0.26, rRMSE = 22.3 ± 8.3%) for walking straight. Smallest mean difference of classical discrete load metrics was seen for KFM impulse, 10.6 ± 47.0%. The results demonstrate the feasibility of using only two IMUs to estimate KFM and KAM to a limited extent. This methodological step facilitates further work that should aim to improve the estimation accuracy to provide valuable biofeedback systems for KOA patients. Greater accuracy of effective implementation could be achieved by a participant- or task-specific ANN modeling.
Neural effects of acute stress on appetite: A magnetoencephalography study

Stress is prevalent in modern society and can affect human health through its effects on appetite. Therefore, in the present study, we aimed to clarify the neural mechanisms by which acute stress affects appetite in healthy, non-obese males during fasting. In total, 22 volunteers participated in two experiments (stress and control conditions) on different days. The participants performed a stress-inducing speech-and-mental-arithmetic task under both conditions, and then viewed images of food, during which, their neural activity was recorded using magnetoencephalography (MEG). In the stress condition, the participants were told to perform the speech-and-mental-arithmetic task again subsequently to viewing the food images; however, another speech-and-mental-arithmetic task was not performed actually. Subjective levels of stress and appetite were then assessed using a visual analog scale. Electrocardiography was performed to assess the index of heart rate variability reflecting sympathetic nerve activity. The findings showed that subjective levels of stress and sympathetic nerve activity were increased in the MEG session in the stress condition, whereas appetite gradually increased in the MEG session only in the control condition. The decrease in alpha band power in the frontal pole caused by viewing the food images was greater in the stress condition than in the control condition. These findings suggest that acute stress can suppress the increase of appetite, and this suppression is associated with the frontal pole. The results of the present study may provide valuable clues to gain a further understanding of the neural mechanisms by which acute stress affects appetite. However, since the stress examined in the present study was related to the expectation of forthcoming stressful event, our present findings may not be generalized to the stress unrelated to the expectation of forthcoming stressful event.
Determination of Complex Small‐Molecule Structures Using Molecular Alignment Simulation

Abstract Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy‐based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule‐specific anisotropic NMR parameters. The quantitative correlation uses an accurate three‐dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ‐benzyl‐l‐glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.
Interaction dynamics between hate and counter users on Twitter

Social media platforms usually tackle the proliferation of hate speech by blocking/suspending the message or account. One of the major drawback of such measures is the restriction of free speech. In this paper, we investigate the interaction of hatespeech and the responses that counter it (aka counter-speech). One of the prime contribution of this work is that we developed and released1 a dataset where we annotate pairs of hate and counter users. We perform several lexical, linguistic and psycholinguistic analysis on these annotated accounts and observe that the couterspeakers of the target communities employ different strategies to tackle the hatespeech. The hate users seem to be more popular as we observe that they are more subjective, express more negative sentiment, tweet more and have more followers. While the hate users seem to use words more about envy, hate, negative emotion, swearing terms, ugliness, the counter users use more words related to government, law, leader. Finally, we build a classifier to detect if a user is a hateful or counter speaker. This identification can help the platform to devise different incentive mechanisms to demote hate and promote counter speakers. Overall, our study unfolds for the first time, the interaction dynamics of the hate and counter users which could pave a more effective way for combating hate content on Twitter than just suspending the hate accounts.
The Unique Antimicrobial Recognition and Signaling Pathways in Tardigrades with a Comparison Across Ecdysozoa

Tardigrades are microscopic animals known to withstand unfavorable abiotic conditions. These animals are also constantly exposed to biotic stresses, including parasites and internal microbiomes. However, the tardigrade immune mechanisms against these biotic stresses are largely uncharacterized. Due to the contentious phylogenetic position of tardigrades, it is not intuitive whether they possess an immune system more similar to that of arthropods (e.g., Toll, Imd, and JNK pathways of the Drosophila melanogaster antimicrobial response) or to that of nematodes (e.g., the Tir-1/Nsy-1/Sek-1/Pmk-1/Atf-7 signaling cassette [called Tir-1 pathway here]) in Caenorhabditis elegans). In this study, comparative genomic analyses were conducted to mine homologs of canonical D. melanogaster and C. elegans immune pathway genes from eight tardigrades (Echiniscoides cf. sigismundi, Echiniscus testudo, Hypsibius exemplaris, Mesobiotus philippinicus, Milnesium tardigradum, Paramacrobiotus richtersi, Richtersius cf. coronifer, and Ramazzottius varieornatus) and four non-arthropod ecdysozoans (two onychophorans: Epiperipatus sp. and Opisthopatus kwazululandi; one nematomorph: Paragordius varius; and one priapulan: Priapulus caudatus) in order to provide insights into the tardigrade antimicrobial system. No homologs of the intracellular components of the Toll pathway were detected in any of the tardigrades examined. Likewise, no homologs of most of the Imd pathway genes were detected in any of the tardigrades or any of the other non-arthropod ecdysozoans. Both the JNK and Tir-1 pathways, on the other hand, were found to be conserved across ecdysozoans. Interestingly, tardigrades had no detectable homologs of NF-κB, the major activator of antimicrobial response gene expression. Instead, tardigrades appear to possess NF-κB distantly related NFAT homologs. Overall, our results show that tardigrades have a unique gene pathway repertoire that differs from that of other ecdysozoans. Our study also provides a framework for future studies on tardigrade immune responses.
Smoking-Related Risks of Colorectal Cancer by Anatomical Subsite and Sex

Abstract The purpose of this study was to examine whether the increased risk of colorectal cancer due to cigarette smoking differed by anatomical subsite or sex. We analyzed data from 188,052 participants aged 45–75 years (45% men) who were enrolled in the Multiethnic Cohort Study in 1993–1996. During a mean follow-up period of 16.7 years, we identified 4,879 incident cases of invasive colorectal adenocarcinoma. In multivariate Cox regression models, as compared with never smokers of the same sex, male ever smokers had a 39% higher risk (hazard ratio (HR) = 1.39, 95% confidence interval (CI): 1.16, 1.67) of cancer of the left (distal or descending) colon but not of the right (proximal or ascending) colon (HR = 1.03, 95% CI: 0.89, 1.18), while female ever smokers had a 20% higher risk (HR = 1.20, 95% CI: 1.06, 1.36) of cancer of the right colon but not of the left colon (HR = 0.96, 95% CI: 0.80, 1.15). Compared with male smokers, female smokers had a greater increase in risk of rectal cancer with number of pack-years of smoking (P for heterogeneity = 0.03). Our results suggest that male smokers are at increased risk of left colon cancer and female smokers are at increased risk of right colon cancer. Our study also suggests that females who smoke may have a higher risk of rectal cancer due to smoking than their male counterparts.
Derivation of new human embryonic stem cell lines (Yazd1-3) and their vitrification using Cryotech and Cryowin tools: A lab resources report

Abstract Background Cell banking of initial outgrowths from newly derived human embryonic stem cells (hESCs) requires an efficient freezing method. Vitrification is used for the preservation of gametes and early embryos in assisted reproduction techniques (ART). Moreover, vitrification was applied for cryopreservation of hESCs using open pulled straws. Objective To derive and characterize new hESC lines and then use Cryotech and Cryowin tools for their vitrification. Materials and Methods Human ESC lines were generated in a microdrop culture system using mouse embryonic fibroblasts (MEFs) as the feeder layer; this was later scaled up using both MEFs and Yazd human foreskin fibroblasts batch 8 (YhFF#8). To bank the cell lines, master cell banks of 100 Cryotech and Cryowin tools were produced for each individual cell line using the vitrification method; flasks of hESC lines were also cryopreserved using a conventional slow-freezing method. Results The pluripotency of cell lines was assessed by their expression of pluripotency-associated genes (OCT4/POU5F1, NANOG, and SOX2) and markers such as SSEA4, TRA-1-60, and TRA-2-49. Their in vitro capacity to differentiate into germ layers and germ cells using embryoid body (EB) formation and monolayer culture was assessed by screening the expression of differentiation-associated genes. The chromosomal constitution of each hESC line was assessed by G-banding karyotyping. Conclusion Cryotech and Cryowin tools used to vitrify new hESCs at an early stage of derivation is an efficient method of preserving hESCs.
Digging the diversity of Iberian bait worms Marphysa (Annelida, Eunicidae)

During a visit to polychaete–rearing facilities in the vicinity of Bay of Cádiz (SW Iberian Peninsula, Atlantic Ocean), we sampled two populations of Marphysa (Annelida, Eunicidae) originally occurring at nearby intertidal soft bottoms, one being more than twice as long as the other at the same age. We analysed them using partial sequences of two mitochondrial genes, 16S rDNA and Cytochrome Oxidase I, and classical morphological observations. Our molecular results confirmed that the two populations corresponded to two different species, with PTP species delimitation values ranging from 0.973 (long–bodied species) to 0.999 (short–bodied species). Morphologically, the short–bodied species resembles the recently redescribed M. sanguinea (Montagu, 1813), but differs mainly in having some parapodia with two subacicular hooks (one bidentate and one unidentate) and three types of pectinate chaetae, Two isodont present all along the body, and one particularly large anodont asymmetric appearing only from mid–posterior parapodia. The long–bodied species resembles Marphysa aegypti Elgetany, El-Ghobashy, Ghoneim and Struck, 2018 both in size and in having very robust, unidentate subacicular hooks (single in most parapodia, two–both similar in size and form–in some posterior parapodia), but differs, among other features, in the maxillary formula, the number of acicula per parapodia and the number and shape of pectinate chaetae. Accordingly, we are here fully illustrating and formally describing the two Iberian populations as Marphysa gaditana sp. nov. (short–bodied) and Marphysa chirigota sp. nov. (long–bodied) and we are emending the description of M. aegypti based on our revision of the type material. Also, we discuss on the distribution of the species of the sanguinea–group and on the relevancy of taxonomically robust studies when dealing with species of commercial interest having the potential of being globally spread through human activities, as well as on the misunderstandings caused by the incorrect use of the “cosmopolitan species” concept.
Pentagram-shaped Ag@Pt core-shell nanostructures as high-performance catalyst for formaldehyde detection.

High performance HCHO sensor is of great importance in various application fields such as indoor air quality (IAQ) assessments. Herein, bimetallic Ag-Pt nanoparticles are synthesized as high-performance catalyst for ZnO-based gas sensors. Spherical aberration (Cs)-corrected transmission electron microscopy (TEM) images with atomic-resolution clearly indicate that the prepared nanoparticles exhibit a novel Ag@Pt core-shell nanostructure with pentagram shape. For high-performance HCHO sensor construction, integrated micro-electrodes are firstly fabricated with microelectromechanical systems (MEMS) technology. Then, hydrothermal route is used to self-assemble well-aligned ZnO nanowire array onto the sensing micro-region. After that, the pentagram-shaped Ag@Pt nanoparticles are loaded onto the surface of ZnO nanowires with ink-jet printing technique to form MEMS sensors with Ag@Pt@ZnO as sensing material. The thoroughly sensing experiments indicate that the Ag@Pt nanoparticles exhibit satisfied catalytic-activation to HCHO molecules. The experimental observed detection limit of our sensor to HCHO reaches parts per billion (ppb) level. To elucidate the HCHO-sensing mechanism, on-line mass spectrum (on-line MS) is utilized to analysis the components of exhaust gas stream of HCHO flowing through the Ag@Pt@ZnO material. The on-line MS indicates that, with Ag@Pt catalyst, HCHO molecules are partially oxidized to HCOOH molecules at low temperature and are completely oxidized to CO2 molecules at high temperature.
High Levels of Epstein–Barr Virus Nuclear Antigen-1-Specific Antibodies and Infectious Mononucleosis Act Both Independently and Synergistically to Increase Multiple Sclerosis Risk

Objective: Elevated levels of anti-EBNA-1 antibodies and infectious mononucleosis (IM) history have consistently been associated with multiple sclerosis (MS) risk. We aimed to study whether these aspects of Epstein–Barr virus (EBV) infection represent separate risk factors for MS and whether they both interact with MS-associated HLA genes in disease development. Methods: Two Swedish-population-based case–control studies were used, comprising 5,316 cases and 5,431 matched controls. Subjects with different HLA alleles, EBNA-1, and IM status were compared regarding MS risk by calculating odds ratios (OR) with 95% confidence intervals (CI) employing logistic regression. Causal mediation analysis was used to assess to what extent the relationship between IM history and MS risk was mediated by high anti-EBNA-1 antibody levels and vice versa. Results: The causal mediation analysis revealed that both aspects of EBV infection mainly act directly on MS risk. The direct effect of elevated anti-EBNA-1 antibody levels on MS risk, expressed on the OR scale, was 2.8 (95% CI 2.5–3.1), and the direct effect of IM history on MS risk was 1.7 (95% CI 1.5–2.0). A significant interaction between the two aspects of EBV infection was observed (RERI 1.2, 95% CI 0.3–2.0), accounting for about 50% of the total effect. Further, both aspects of EBV infection interacted with DRB1*15:01 and absence of A*02:01. Interpretation: Elevated anti-EBNA-1 antibody levels and IM history are different risk factors for MS. The two aspects of EBV infection act synergistically to increase MS risk, indicating that they partly are involved in the same biological pathways.
DIABETIC RETINOPATHY, CLASSIFIED USING THE LESION-AWARE DEEP LEARNING SYSTEM, PREDICTS DIABETIC END-STAGE RENAL DISEASE IN CHINESE PATIENTS.

Aims: To characterize the relationship between diabetic retinopathy (DR) and diabetic nephropathy (DN) in Chinese patients and to determine whether the severity of DR predicts end-stage renal disease (ESRD). Methods: Bilateral fundic photographs of 91 Chinese type 2 diabetic patients with biopsy-confirmed DN, not in ESRD stage, were obtained at the time of renal biopsy in this longitudinal study. The baseline severity of DR was determined using the Lesion-aware Deep Learning System (RetinalNET) in an open framework for deep learning and was graded using the Early Treatment Diabetic Retinopathy Study Severity Scale. Cox proportional hazard models were used to estimate the hazard ratio (HR) for the effect of the severity of diabetic retinopathy on ESRD. Results: During a median follow-up of 15 months, 25 patients progressed to ESRD. The severity of retinopathy at the time of biopsy was a prognostic factor for progression to ESRD (HR 2.18, 95% confidence interval (CI) 1.05-4.53, P= 0.04). At baseline, more severe retinopathy was associated with poor renal function, and more severe glomerular lesions. However, 30% patients with mild retinopathy and severe glomerular lesions had higher low-density lipoprotein-cholesterol and more severe proteinuria than those with mild glomerular lesions. Additionally, 3% of patients with severe retinopathy and mild glomerular changes were more likely to have had diabetes a long time than those with severe glomerular lesions. Conclusions: Although the severity of DR predicted diabetic ESRD in patients with T2DM and DN, the severities of DR and DN were not always consistent, especially in patients with mild retinopathy or microalbuminuria.
Resistance of Amaranthus Spp. to the Green Peach Aphid (Hemiptera: Aphididae)

Abstract The green peach aphid [Myzus persicae (Sulzer)] is an important pest of amaranth grown for leaf consumption (i.e., leafy amaranth) in the tropics. Aphids reduce the amount of fresh leaf yield of amaranth and the value of leafy amaranth as aphid-infested leaves are not marketable. Our objective was to evaluate Amaranthus species selected by a breeding program in East Africa to develop cultivars for leaf consumption with resistance to M. persicae. We focused on antibiosis to determine whether varieties of Amaranthus spp. could be grown without producing an aphid population. Artificial infestations of aphids were placed on multiple selections of three species of Amaranthus: two selections of A. blitum, four selections of A. hybridus and one selection of A. hypochondriacus. Aphid populations were assessed over a 5-wk period. Evaluations of vegetative yield, leaf damage symptoms, and specific leaf area (SLA) were made of the seven selections at the end of this experiment. Aphid populations assessed 49 d after planting differed significantly (P ≤ 0.001) among the amaranth species and within selections of the same species.The selections of A. blitum had the lowest aphid populations, and A. hybridus had the highest populations. Selections of A. hybridus produced the most marketable leaves (i.e., aphid free). The fresh weight of A. blitum were the lowest of the seven selections, whereas A. hybridus had the greatest fresh leaf weight. Implications of these finding for further promotion of amaranth breeding are discussed related to pest management for leaf production.
Putting Research-based Machine Learning Solutions for Subject Indexing into Practice

Subject indexing, i.e., the enrichment of metadata records for textual resources with descriptors from a controlled vocabulary, is one of the core activities of libraries. However, due to the proliferation of digital documents it is no longer possible to annotate every single document intellectually, which is why we need to explore the potentials of automation. At ZBW the efforts to partially or completely automate the subject indexing process have started around the year 2000 but the prototypical machine learning solutions that we developed in an applied research project over the past few years have yet to be integrated into productive operations at the library. In this short paper, we outline the challenges that we perceive and the steps that we are taking towards completing the transfer of our solutions into practice – in particular, we are in the process of specifying what a suitable architecture for that task should look like and establishing a roadmap for the next two years indicating the milestones that have to be reached in order to build and test that architecture and to subsequently ensure its availability and continuous development during running operations.