Miracle-dz/UniFAR-FTUs huggingface dataset:
Perceived stress may mediate the relationship between antenatal depressive symptoms and preterm birth: A pilot observational cohort study

Background Screening for changes in pregnancy-related anxiety and depressive symptoms during pregnancy may further our understanding of the relationship between these two variables and preterm birth. Objectives To determine whether changes in pregnancy-related anxiety and depressive symptoms during pregnancy influence the risk of preterm birth among Pakistani women; explore whether perceived stress moderates or mediates this relationship, and examine the relationship between the various components of pregnancy-related anxiety and preterm birth. Methods A prospective cohort study design was used to recruit a diverse sample of 300 low-risk pregnant women from four centers of Aga Khan Hospital for Women and Children in Karachi, Pakistan. Changes in pregnancy-related anxiety and depressive symptoms during pregnancy were tested. Multiple logistic regression analysis was used to determine a predictive model for preterm birth. We then determined if the influence of perceived stress could moderate or mediate the effect of depressive symptoms on preterm birth. Results Changes in pregnancy-related anxiety (OR = 1.1, CI 0.97–1.17, p = 0.167) and depressive symptoms (OR = 0.9, CI 0.85–1.03, p = 0.179) were insignificant as predictors of preterm birth after adjusting for the effects of maternal education and family type. When perceived stress was added into the model, we found that changes in depressive symptoms became marginally significant after adjusting for covariates (OR = 0.9, CI 0.82–1.01, p = 0.082). After adjusting for the mediation effect of change in perceived stress, the effect of change in depressive symptoms on preterm birth were marginally significant after adjusting for covariates. Among six different dimensions of pregnancy-related anxiety, mother’s concerns about fetal health showed a trend towards being predictive of preterm birth (OR = 1.3, CI 0.97–1.72, p = 0.078). Conclusions There may be a relationship between perceived stress and antenatal depressive symptoms and preterm birth. This is the first study of its kind to be conducted in Pakistan. Further research is required to validate these results.
Spatial regulation of protein A in Staphylococcus aureus

Surface proteins of Staphylococcus aureus play vital roles in bacterial physiology and pathogenesis. Recent work suggests that surface proteins are spatially regulated by a YSIRK/GXXS signal peptide that promotes cross‐wall targeting at the mid‐cell, though the mechanisms remain unclear. We previously showed that protein A (SpA), a YSIRK/GXXS protein and key staphylococcal virulence factor, mis‐localizes in a ltaS mutant deficient in lipoteichoic acid (LTA) production. Here, we identified that SpA contains another cross‐wall targeting signal, the LysM domain, which, in addition to the YSIRK/GXXS signal peptide, significantly enhances SpA cross‐wall targeting. We show that LTA synthesis, but not LtaS, is required for SpA septal anchoring and cross‐wall deposition. Interestingly, LTA is predominantly found at the peripheral cell membrane and is diminished at the septum of dividing staphylococcal cells, suggesting a restriction mechanism for SpA septal localization. Finally, we show that D‐alanylation of LTA abolishes SpA cross‐wall deposition by disrupting SpA distribution in the peptidoglycan layer without altering SpA septal anchoring. Our study reveals that multiple factors contribute to the spatial regulation and cross‐wall targeting of SpA via different mechanisms, which coordinately ensures efficient incorporation of surface proteins into the growing peptidoglycan during the cell cycle.
Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60–14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3′-endo to C2′-endo) upon pulling ssDNA.
Contribution of Interleukin-10 Genotype to Triple Negative Breast Cancer Risk

Background/Aim: Triple negative breast cancer (TNBC) is characterized by increased recurrence and poor survival. Mounting evidence suggests that interleukin-10 (IL-10) plays a role in carcinogenesis, however, little is known about the contribution of IL-10 to TNBC. The study evaluated the contribution of IL-10 promoter A-1082G (rs1800896), T-819C (rs3021097), A-592C (rs1800872) genotypes to the risk of TNBC. Materials and Methods: IL-10 genotypes were examined among 1,232 breast cancer patients and 1,232 controls and evaluated. Results: The percentages of AG and GG for IL-10 A-1082G genotypes were higher in the breast cancer patient group than in the control group. The GG genotype carriers were of higher risk for breast cancer [odds ratio (OR)=2.02, 95% confidence interval (CI)=1.28-3.21, p=0.0021]. Interestingly, G allele carriers were of higher risk of TNBC (OR=1.25, 95%CI=1.07-1.46, p=0.0050). Conclusion: The G allele of IL-10 A-1082G genotype may serve as a predictor for TNBC risk. The finding should be validated in other populations.
Modulation of Apoptosis and Epithelial-Mesenchymal Transition E-cadherin/TGF-β/Snail/TWIST Pathways by a New Ciprofloxacin Chalcone in Breast Cancer Cells

Background/Aim: This study aimed to investigate the effect of the new ciprofloxacin chalcone [7-(4-(N-substituted carbamoyl methyl) piperazin-1 yl)] on the proliferation, migration, and metastasis of MCF-7 and MDA-MB-231 breast cancer cell lines. Materials and Methods: Cell viability, colony formation and cell migration abilities were analysed. Cell cycle distribution and apoptosis were examined by flow cytometry. The molecular mechanism underlying chalcone’s activity was investigated using qRT-PCR and western blotting. Results: This new ciprofloxacin chalcone significantly inhibited proliferation, colony formation, and cell migration abilities of both cancer cell lines. Furthermore, it initiated apoptosis and caused cell cycle arrest at G2/M and S phase in MCF-7 and MDA-MB-231 cell lines, respectively. In addition, it up-regulated the expression of pro-apoptotic factors, p53, PUMA and NOXA, and down-regulated the expression of anti-apoptotic factors, MDM2 and MDM4. At the same time, it inhibited epithelial–mesenchymal transition by increasing the expression of E-cadherin and decreasing the expression of TGF-β1, SNAI1, TWIST1, MMP2, and MMP9. Conclusion: This new ciprofloxacin chalcone exhibited promising apoptotic and anti-metastatic activities against MCF-7 and MDA-MB-231 breast cancer cell lines, and, therefore, is an attractive molecule for drug development in the treatment of breast cancer.
Comparison of Physician-recorded Toxicities and Patient-reported Outcomes of Five Different Radiotherapy Methods for Prostate Cancer

Background/Aim: To compare five radiotherapy methods for prostate cancer. Patients and Methods: During 2005-2018, the data of patients with non-metastatic prostate cancer were retrospectively analysed. Patients were treated with high-dose-rate brachytherapy (HDR-BT); low-dose-rate brachytherapy (LDR-BT); or external-beam radiotherapy (EBRT), including conventionally fractionated radiotherapy (CFRT), moderate-hypofractionated radiotherapy (MHRT), and ultra-hypofractionated radiotherapy (UHRT). Results: In total, 496 patients (149, HDR-BT; 100, LDR-BT; 100, CFRT; 97, MHRT, and 50, UHRT) with a median follow-up of 4.3 years were enrolled. The incidence of grade ≥2 acute genitourinary toxicities was significantly lower with HDR-BT (p<0.001) than with any other radiotherapy. The cumulative incidence of late grade ≥2 genitourinary toxicities was the highest with UHRT and significantly higher (p=0.005) with UHRT than with HDR-BT. Higher symptom score peaks were noted 4 weeks after therapy for LDR-BT than for EBRT. Conclusion: Physician-recorded toxicities were slightly lower with HDR-BT and patient-reported outcomes tended to be worse with LDR-BT.
Wearable Devices: Current Status and Opportunities in Pain Assessment and Management

Introduction: We investigated the possibilities and opportunities for using wearable devices that measure physical activity and physiometric signals in conjunction with ecological momentary assessment (EMA) data to improve the assessment and treatment of pain. Methods: We considered studies with cross-sectional and longitudinal designs as well as interventional or observational studies correlating pain scores with measures derived from wearable devices. A search was also performed on studies that investigated physical activity and physiometric signals among patients with pain. Results: Few studies have assessed the possibility of incorporating wearable devices as objective tools for contextualizing pain and physical function in free-living environments. Of the studies that have been conducted, most focus solely on physical activity and functional outcomes as measured by a wearable accelerometer. Several studies report promising correlations between pain scores and signals derived from wearable devices, objectively measured physical activity, and physical function. In addition, there is a known association between physiologic signals that can be measured by wearable devices and pain, though studies using wearable devices to measure these signals and associate them with pain in free-living environments are limited. Conclusion: There exists a great opportunity to study the complex interplay between physiometric signals, physical function, and pain in a real-time fashion in free-living environments. The literature supports the hypothesis that wearable devices can be used to develop reproducible biosignals that correlate with pain. The combination of wearable devices and EMA will likely lead to the development of clinically meaningful endpoints that will transform how we understand and treat pain patients.
5′ ALK Amplification in Neuroblastoma: A Case Report

Neuroblastoma is the most common cancer in infants younger than 12 months of age, occurring with an incidence of 1 in 100,000 children. The clinical outcome of neuroblastoma ranges from spontaneous regression to treatment-resistant progression and/or metastasis, and accounts for 8–10% of childhood cancer deaths. Segmental chromosomal aberrations, as well as MYCN and ALK amplification, are among factors contributing to an unfavorable genomic profile and high-risk disease classification. Here, we describe a 5-year-old male who presented with a large right renal neuroblastoma tumor having lung and liver metastases. Fluorescence in situ hybridization analysis indicated the presence of >20 copies of the 5′ region of the ALK gene in 26% of cells examined. Subsequent copy number assessment did not confirm ALK amplification, but revealed a gain of exons 2–5 of ALK, consistent with increased copy number for the 5′ region of the ALK gene. Subsequent array analysis showed the presence of other unfavorable prognostic genomic features, including segmental gain of the 17q region and amplification of the long arm of chromosome 12 harboring CDK4 and MDM2, both reported to be poor prognostic indicators in patients with atypical clinical features in neuroblastoma. Taken together, this report illustrates the importance of careful interpretation of aberrant FISH findings and subsequent use of orthogonal methods to clarify the presence of genomic alterations to successfully determine potential treatment targets.
Décomposition de domaine pour la simulation Full-Wave dans un plasma froid

De nos jours, les centrales nucleaires produisent de l'energie par des reactions de fission (division d'un noyau atomique lourd en plusieurs noyaux atomiques legers et neutrons). Une alternative serait d'utiliser plutot la reaction de fusion de noyaux legers de deuterium et de tritium, isotopes de l'hydrogene. Toutefois, cette technique reste encore du domaine de la recherche en physique des plasmas. Les experiences effectuees dans ce domaine ont revele que les reacteurs a configuration magnetique toroidale, dite tokamak, sont les plus efficaces. Un melange gazeux d'isotopes de l'hydrogene appele plasma est confine grâce a un champ magnetique produit par des bobines. Ce plasma doit etre chauffe a une temperature tres elevee afin que les reactions de fusion aboutissent. De meme, un courant intense doit etre maintenu dans le plasma afin d'obtenir une configuration magnetique qui permet de le confiner. Une des methodes les plus attrayantes parmi les techniques connues pour generer du courant est basee sur l'injection d'ondes electromagnetiques dans le plasma a la frequence proche de la resonance hybride. Cette methode offre la possibilite de controler le profil de densite dans le plasma. Une analyse de type Full-Wave permet alors de modeliser la propagation et l'absorption de l'onde hybride a partir des equations de Maxwell. Le but de cette these est de developper une methode numerique pour cette simulation Full-Wave. Le chapitre 2 presente les equations de propagation d'ondes en mettant en evidence les caracteres physiques du plasma. Une approche variationnelle de type mixte augmentee est developpee et une analyse mathematique de cette derniere est effectuee dans le chapitre 3. Dans le contexte de la geometrie d'un tokamak, le probleme Full-Wave dependant de trois parametres peut etre reduit en une serie de problemes a deux variables a l'aide de la transformation de Fourier, ce sera l'objet du chapitre 4. Dans le chapitre 5, la formulation variationnelle obtenue a partir du probleme mode par mode est discretisee en utilisant des elements finis nodaux de type Taylor-Hood. Le chapitre 6 concerne les methodes de resolution du systeme lineaire apres discretisation. A l'aide de differents diagnostics physiques presentes dans le chapitre 7, des resultats de la simulation Full-Wave obtenues a partir d'un code MATLAB sont presentees dans le chapitre 8. Enfin, dans le but de developper une version parallele de la simulation, le chapitre 9 est consacre a une methode de decomposition de domaine sans recouvrement associe au systeme Full-Wave.
Expression of Oligodendrocyte and Oligoprogenitor Cell Proteins in Frontal Cortical White and Gray Matter: Impact of Adolescent Development and Ethanol Exposure

Adolescent development of prefrontal cortex (PFC) parallels maturation of executive functions as well as increasing white matter and myelination. Studies using MRI and other methods find that PFC white matter increases across adolescence into adulthood in both humans and rodents. Adolescent binge drinking is common and has been found to alter adult behaviors and PFC functions. This study examines development of oligoprogenitor (OPC) and oligodendrocytes (OLs) in Wistar rats from adolescence to adulthood within PFC white matter, corpus callosum forceps minor (fmi), PFC gray matter, and the neurogenic subventricular zone (SVZ) using immunohistochemistry for marker proteins. In addition, the effects of adolescent intermittent ethanol exposure [AIE; 5.0 g/kg/day, intragastric, 2 days on/2 days off on postnatal day (P)25–54], which is a weekend binge drinking model, were determined. OPC markers NG2+, PDGFRα+ and Olig2+IHC were differentially impacted by both age and PFC region. In both fmi and SVZ, NG2+IHC cells declined from adolescence to adulthood with AIE increasing adult NG2+IHC cells and their association with microglial marker Iba1. PFC gray matter decline in NG2+IHC in adulthood was not altered by AIE. Both adult maturation and AIE impacted OL expression of PLP+, MBP+, MAG+, MOG+, CNPase+, Olig1+, and Olig2+IHC in all three PFC regions, but in region- and marker-specific patterns. These findings are consistent with PFC region-specific changes in OPC and OL markers from adolescence to adulthood as well as following AIE that could contribute to lasting changes in PFC function.
The Limits of Language-Thought Influences Can Be Set by the Constraints of Embodiment

Language and thought are intimately related to one another, but the level or degree of connectedness between language and thought is not clear due to the fact that the influence of language over thought can be more context-specific or general (see Zlatev and Blomberg, 2015). This reflects general assumptions from the Sapir–Whorf Hypothesis (Whorf, 1956). If the influence of language over thought, thinking, and reasoning is very context-specific in being applicable to specific modes/modalities of cognition, such as color, space, visual motion, etc., this may suggest that the constraints of embodiment determine how modal linguistic symbols come to be grounded in neurally instantiated modality-specific systems (Barsalou, 2008).
Voxel-Based State Space Modeling Recovers Task-Related Cognitive States in Naturalistic fMRI Experiments

Complex natural tasks likely recruit many different functional brain networks, but it is difficult to predict how such tasks will be represented across cortical areas and networks. Previous electrophysiology studies suggest that task variables are represented in a low-dimensional subspace within the activity space of neural populations. Here we develop a voxel-based state space modeling method for recovering task-related state spaces from human fMRI data. We apply this method to data acquired in a controlled visual attention task and a video game task. We find that each task induces distinct brain states that can be embedded in a low-dimensional state space that reflects task parameters, and that attention increases state separation in the task-related subspace. Our results demonstrate that the state space framework offers a powerful approach for modeling human brain activity elicited by complex natural tasks.
EAAT5 Glutamate Transporter-Mediated Inhibition in the Vertebrate Retina

Glutamate transporters typically remove glutamate from the synaptic cleft. In addition, all glutamate transporters have a chloride channel, which is opened upon glutamate binding to the transporter. There are five types of glutamate transporter (EAATs 1–5, excitatory amino acid transporters), which have distinct chloride conductances. Some EAATs that have low chloride conductances, remove glutamate from the synaptic cleft most effectively (e.g., EAAT1). By contrast, EAATs that have high chloride conductances, remove glutamate less effectively (e.g., EAAT5). We have studied EAAT5 in the retina. In the retina, light activates a chloride current, mediated by the glutamate activation of EAAT5. EAAT5 is not a significant contributor to lateral inhibition in the retina. Instead, it is the main source of autoinhibition to rod bipolar cells (RBCs). EAAT5-mediated inhibition has a substantial effect on synaptic transmission from RBCs to downstream retinal neurons.
Enhanced Anaerobic Biogas Production From Wheat Straw by Herbal-Extraction Process Residues Supplementation

Trace metals are essential constituents of cofactors and enzymes and that their addition to anaerobic digesters increases methane production. Many trace elements are contained in herbal-extraction process residues (HPR). The present study concerns the effect of six kinds of HPR [Danshen root (Dr), Astragalus membranaceus (Am), Isatis root (Ir), Angelica sinensis (As), and Pseudo-ginseng (Pg)] that were used as additives, respectively, in the anaerobic digestion of wheat straw on biogas and methane production. The ratios of HPR residues/wheat straw [based on total solids (TS), of wheat straw] were 3, 5, and 10%, respectively. The digesters were at 37 ± 1°C of water bath during 30 days of anaerobic digestion. The results showed that HPR had significant effects on the anaerobic co-digestion. The highest biogas productivity was achieved when treated with 10% Pseudo-ginseng residues (PGR), which yielded 337 ml/g TS of biogas and 178 ml/g TS of methane. Cumulative production of biogas and methane increased by 28 and 37% compared to the production achieved in the control. These results suggest that PGR is an effective HPR to enhance the production of methane.
Polynomial, piecewise-Linear, Step (PLS): A Simple, Scalable, and Efficient Framework for Modeling Neurons

Biological neurons can be modeled with different levels of biophysical/biochemical details. The accuracy with which a model reflects the actual physiological processes and ultimately the information function of a neuron, can range from very detailed to a schematic phenomenological representation. This range exists due to the common problem: one needs to find an optimal trade-off between the level of details needed to capture the necessary information processing in a neuron and the computational load needed to compute 1 s of model time. An increase in modeled network size or model-time, for which the solution should be obtained, makes this trade-off pivotal in model development. Numerical simulations become incredibly challenging when an extensive network with a detailed representation of each neuron needs to be modeled over a long time interval to study slow evolving processes, e.g., development of the thalamocortical circuits. Here we suggest a simple, powerful and flexible approach in which we approximate the right-hand sides of differential equations by combinations of functions from three families: Polynomial, piecewise-Linear, Step (PLS). To obtain a single coherent framework, we provide four core principles in which PLS functions should be combined. We show the rationale behind each of the core principles. Two examples illustrate how to build a conductance-based or phenomenological model using the PLS-framework. We use the first example as a benchmark on three different computational platforms: CPU, GPU, and mobile system-on-chip devices. We show that the PLS-framework speeds up computations without increasing the memory footprint and maintains high model fidelity comparable to the fully-computed model or with lookup-table approximation. We are convinced that the full range of neuron models: from biophysical to phenomenological and even to abstract models, may benefit from using the PLS-framework.