Miracle-dz/UniFAR-FTUs huggingface dataset:
A mathematical model for cell cycle control: graded response or quantized response

ABSTRACT Cell cycle is an important and complex biological system. A lot of efforts have been put in understanding cell cycle arrest for its vital role in clinical therapies. The cell-cycle-arrest outcomes upon stimulation are complicated. The response could be stringent or relaxed, and graded or quantized. A model fully addressing various cell-cycle-arrest outcomes is to be developed. Here, we developed a mathematical model of cell cycle control incorporating distinct characteristics of various cell-cycle-arrest outcomes. The model can simulate two typical properties of cell cycle arrest, quantized and graded. We also characterized the inheritable quiescence and refractory state, which were crucial in long-term response of the population. Then, we monitored cells respond to multiple stimulations, and the results indicated that cells responded to stimulations with small interval did not induce significantly sustained cell cycle arrest as the existence of refractory state. Our work will benefit fundamental research and make efforts to predicting outcomes of clinical therapeutics.
The Vital Role of CHWs During the COVID-19 Pandemic within the South Texas Communities

To date, Texas has had over 4 million cases of infections and more than 74,000 deaths from the novel coronavirus disease (COVID-19) (Texas Department of State Health Services, 2021). The COVID-19 pandemic has exposed frontline healthcare workers to unprecedented situations thereby causing them to experience psychological distress and burnout (Gupta & Sahoo, 2020). The ever-increasing number of confirmed and suspected cases, overwhelming workload, understaffed personnel, risk of exposure to the infection, as well as feelings of isolation due to social distancing measures are contributing to high rates of depression, anxiety, post-traumatic stress, and insomnia to frontline healthcare workers (Gupta & Sahoo, 2020; Pappa et al., 2020). Much of the research and the literature we found about the mental health of frontline healthcare workers during the COVID-19 pandemic were focused on nurses, physicians, and first responders. Research involving other frontline healthcare workers such as CHWs is largely absent. Although a growing body of literature exists, the need to better understand the mental health consequences of the COVID-19 pandemic as a whole on frontline healthcare workers, including CHWs, is indicated. Doing so could result in the development of effective programs that can deliver mental health support to all frontline healthcare workers, including CHWs.
Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS

Abstract Attaining sufficient tissue exposure at the site of action to achieve the desired pharmacodynamic effect on a target is an important determinant for any drug discovery program, and this can be particularly challenging for oligonucleotides in deep tissues of the CNS. Herein, we report the synthesis and impact of stereopure phosphoryl guanidine-containing backbone linkages (PN linkages) to oligonucleotides acting through an RNase H-mediated mechanism, using Malat1 and C9orf72 as benchmarks. We found that the incorporation of various types of PN linkages to a stereopure oligonucleotide backbone can increase potency of silencing in cultured neurons under free-uptake conditions 10-fold compared with similarly modified stereopure phosphorothioate (PS) and phosphodiester (PO)-based molecules. One of these backbone types, called PN-1, also yielded profound silencing benefits throughout the mouse brain and spinal cord at low doses, improving both the potency and durability of response, especially in difficult to reach brain tissues. Given these benefits in preclinical models, the incorporation of PN linkages into stereopure oligonucleotides with chimeric backbone modifications has the potential to render regions of the brain beyond the spinal cord more accessible to oligonucleotides and, consequently, may also expand the scope of neurological indications amenable to oligonucleotide therapeutics.
Orienting to fear under transient focal disruption of the human amygdala

Abstract Responding to threat is under strong survival pressure, promoting the evolution of systems highly optimized for the task. Though the amygdala is implicated in ‘detecting’ threat, its role in the action that immediately follows—‘orienting’—remains unclear. Critical to mounting a targeted response, such early action requires speed, accuracy, and resilience optimally achieved through conserved, parsimonious, dedicated systems, insured against neural loss by a parallelized functional organization. These characteristics tend to conceal the underlying substrate not only from correlative methods but also from focal disruption over time scales long enough for compensatory adaptation to take place. In a study of six patients with intracranial electrodes temporarily implanted for the clinical evaluation of focal epilepsy, we investigated gaze orienting to fear during focal, transient, unilateral direct electrical disruption of the amygdala. We showed that the amygdala is necessary for rapid gaze shifts towards faces presented in the contralateral hemifield regardless of their emotional expression, establishing its functional lateralization. Behaviourally dissociating the location of presented fear from the direction of the response, we implicated the amygdala not only in detecting contralateral faces, but also in automatically orienting specifically towards fearful ones. This salience-specific role was demonstrated within a drift-diffusion model of action to manifest as an orientation bias towards the location of potential threat. Pixel-wise analysis of target facial morphology revealed scleral exposure as its primary driver, and induced gamma oscillations—obtained from intracranial local field potentials—as its time-locked electrophysiological correlate. The amygdala is here reconceptualized as a functionally lateralized instrument of early action, reconciling previous conflicting accounts confined to detection, and revealing a neural organisation analogous to the superior colliculus, with which it is phylogenetically kin. Greater clarity on its role has the potential to guide therapeutic resection, still frequently complicated by impairments of cognition and behaviour related to threat, and inform novel focal stimulation techniques for the management of neuropsychiatric conditions.
UK clinical and community psychology: Exploring personal and professional connections

Abstract This paper explores the personal and professional connections between clinical psychologists in the United Kingdom (UK) and critical/community psychology (CCP). Specifically, it asks how clinical psychologists define the area, how they relate to it and how they apply it in their work. Twenty clinical psychologists responded to an online survey, 12 of whom went on to take part in a follow‐up telephone interview. Data were analysed using inductive thematic analysis. The results are divided into three sections: i. “describing CCP”: social justice and a questioning stance are considered, ii. “relating to CCP”: an interplay between lifespan events and personal responses are described and iii. “applying CCP”: a dynamic between role‐specific applications and reality checks that either enable or constrain is illustrated. Although the continued need for a CCP is described, the results highlight both challenges and tensions of practising CCP within clinical psychology.
Infant sex differences in human milk intake and composition from 1- to 3-month post-delivery in a healthy United States cohort

Abstract Background Macronutrient composition of human milk differs by infant sex, but few studies have examined sex differences in other milk components, or their potential modification by maternal body mass index (BMI). Aim We compared milk intake and human milk hormone and cytokine concentrations at 1- and 3-month post-delivery and tested infant sex by maternal BMI (OW/OB vs. NW) interactions. Subjects and method Data were analysed for 346 mother–infant dyads in the Mothers and Infants Linked for Healthy Growth (MILk) Study at 1- and 3-month post-delivery. Infant milk intake was estimated by the change in infant weight after test feedings. Concentrations of glucose, insulin, leptin, adiponectin, interleukin-6 (IL-6), and C-reactive protein (CRP) were measured using ELISA. Multivariable linear regression and linear mixed models were used to estimate sex main effects and their interaction with maternal BMI. Results Mean glucose concentration at 1 month was 2.62 mg/dl higher for male infants, but no difference at 3 months was observed. Milk intake and concentrations for the other milk components were similar for males and females at both time points. Associations with infant sex did not differ significantly by maternal BMI. Conclusions Among healthy United States mother–infant dyads, appetite, and growth-regulating factors in human milk did not differ significantly by infant sex.
Sex differences in cardiovascular risk may be related to sex differences in diet patterns: a narrative review

Abstract Context Cardiovascular disease (CVD) is the leading cause of death in the United States and globally. The social and biological differences in diet patterns among men and women may play a role in their differential cardiovascular risk. Objective To describe the dietary patterns associated with CVD risk and investigate the differences in diet patterns between men and women, if these differences affect cardiovascular risk, and to explore potential mechanisms of action. Methods Diet patterns associated with CVD risk were described based on epidemiological and experimental trials. Observational and experimental studies together with systematic and non-systematic reviews were synthesised to examine sex differences in diet and cardiovascular risk factors. Results Differences in vasculature and body composition between sexes may be mediated by dissimilarities in adherence to diet patterns and nutrient metabolism. Salt sensitivity and breakdown and storage of lipids may account for some differences in CVD risk between men and women. Sex differences in social norms, cognitive processing, and odour perception may be affected by biological differences and contribute to differences in cardiovascular risk and dietary patterns. Conclusion The relation between diet patterns and cardiovascular risk is well-established and sex differences in diet patterns likely differentially affect CVD risk between men and women.
The oxidation status of three types of duck meat (conventional, organic, wild) during refrigerated storage under air and vacuum-packaged atmospheres

ABSTRACT 1. This study evaluated and compared the oxidation status of meat from conventionally-farmed, organic and wild ducks during chilled storage in air or vacuum packaging. In total, 48 carcases from each group of ducks were investigated, and 24 carcases from each type of production were stored under vacuum or in air at 3°C ± 1°C. Sample analyses were conducted after 1, 3, 6 and 9 d of storage. 2. The antioxidant capacity (2,2-diphenyl-1-picrylhydrazyl: DPPH), thiobarbituric acid reactive substances (TBARS) and free fatty acids in the breast, thigh and wing muscles were determined. 3. The antioxidant capacity of meat from conventional ducks was higher than that from organic and wild ducks. The muscles of organic and wild ducks were more susceptible to secondary oxidation (particularly when stored in air) than conventionally-raised birds. The free fatty acid levels in samples of breast and thigh meat from wild ducks on the last day of storage were higher than in conventional and organic ducks. 4. The results showed that the oxidation status of meat from conventional ducks was more stable during refrigerated storage than the meat of organic and wild ducks.
Validating the Cambridge Protocol: Reliability of Hip Muscle Strength Measurements Using a Motorized Dynamometer and Electromyography

Background: Muscle weakness is common after injury in athletes and in the presence of hip pathology. It will cause abnormal hip biomechanics and can predict future injury. However, objective measurement of hip muscle strength is difficult to perform accurately and reliably. Therefore, it is challenging to determine when an athlete has returned to preinjury levels of strength. In addition, there is currently no standardized method of obtaining measurements, which prevents the data being compared or shared between research centers. Purpose: The purpose of this study is to comprehensively assess the inter- and intraobserver reliability of our standardized muscle strength measurement protocol. Study Design: Descriptive laboratory study. Level of Evidence: Level 3, inception cohort study. Methods: A total of 16 healthy male volunteers (age = 28.3 ± 7.9 years) were recruited. Those with a previous history of hip injuries or disorders were excluded. These volunteers underwent strength testing according to the Cambridge Protocol on 4 separate occasions, performed by 2 independent assessors. Maximal voluntary contractions, fatigue torque fluctuations, and electromyography measurements were recorded. Intra- and interobserver reliability was assessed using intraclass correlation coefficient (ICC). Results: Good-to-excellent correlation was seen for both intra- and interobserver reliability across almost all hip movements for maximal contractions: ICC ranged 0.78 to 0.93 and 0.78 to 0.96, respectively. The standard error of the mean for all hip movements was also extremely low at 2% to 3%. Conclusion: The Cambridge Protocol is a highly reliable method for objective measurement of hip muscle strength. We recommend future studies use this protocol, or the principles underpinning it, to enable data sharing and comparison across different studies. Clinical Relevance: This is a description and analysis of hip muscle strength measurement. If widely used, it will allow for accurate and objective strength assessment and closer monitoring of hip injuries and pathology.
The stem rust effector protein AvrSr50 escapes Sr50 recognition by a substitution in a single surface‐exposed residue

Summary Pathogen effectors are crucial players during plant colonisation and infection. Plant resistance mostly relies on effector recognition to activate defence responses. Understanding how effector proteins escape from plant surveillance is important for plant breeding and resistance deployment. Here we examined the role of genetic diversity of the stem rust (Puccinia graminis f. sp. tritici (Pgt)) AvrSr50 gene in determining recognition by the corresponding wheat Sr50 resistance gene. We solved the crystal structure of a natural variant of AvrSr50 and used site‐directed mutagenesis and transient expression assays to dissect the molecular mechanisms explaining gain of virulence. We report that AvrSr50 can escape recognition by Sr50 through different mechanisms including DNA insertion, stop codon loss or by amino‐acid variation involving a single substitution of the AvrSr50 surface‐exposed residue Q121. We also report structural homology of AvrSr50 to cupin superfamily members and carbohydrate‐binding modules indicating a potential role in binding sugar moieties. This study identifies key polymorphic sites present in AvrSr50 alleles from natural stem rust populations that play important roles to escape from Sr50 recognition. This constitutes an important step to better understand Pgt effector evolution and to monitor AvrSr50 variants in natural rust populations.
Antibody course and memory B-cell response in the first year after SARS-CoV-2 infection

Abstract Background The possibility of repeat infections with SARS-CoV-2 raises questions regarding quality and longevity of the virus-induced immune response. Methods The antibody course and memory B-cell (MBC) response against SARS-CoV-2 proteins, influenza virus nucleoprotein (NP) and tetanus toxin (Ttx) were examined in adults with mild to moderate SARS-CoV-2 infection in the first year after infection. Results The concentration of SARS-CoV-2 RBD-specific antibodies was low compared with the concentration of influenza virus NP-specific antibodies. The SARS-CoV-2 RBD antibody half-life increased from 95 days in the first six months to 781 days after 9-12 months. The SARS-CoV-2 NP antibody half-life increased from 88 to 248 days. Two thirds of the subjects had SARS CoV-2-specific MBC responses 12 months after infection. SARS-CoV-2 antibody levels correlated with the MBC frequency at 12 months. Conclusions The low concentration of SARS-CoV-2 spike protein antibodies indicates that re-exposure to the virus or vaccination are required to use the B-cell immunity to full capacity. The existence of a robust SARS CoV-2 MBC response at 12 months in most subjects and the substantially increasing antibody half-life provide evidence that the immune response is developing into long-term immunity. The early antibody reaction and the ensuing MBC response are interdependent.
Referrals from community optometrists in England and their replies: A mixed methods study

Community optometrists, through routine eye examinations, identify patients with disease or ocular abnormalities requiring referral to the Hospital Eye Service. In many cases no reply to the referral letter is received, resulting in some patients being re‐referred unnecessarily, potentially increasing the number of other patients who lose sight whilst on hospital waiting lists. This study investigated, qualitatively and quantitatively, factors influencing optometric referrals and replies.
Review of HPLC-MS methods for the analysis of nicotine and its active metabolite cotinine in various biological matrices.

In recent years, tobacco smoking is a risk factor for a series of diseases including cardiovascular diseases, cerebrovascular diseases, and cancers. Nicotine, the primary component of tobacco smoke, is mainly transformed to its active metabolite cotinine, which is often used as biomarker for tobacco exposure for its higher blood concentration and longer residence time than nicotine. Various analytical methods have been developed for the determination of nicotine and cotinine in biological matrices. This article reviewed the HPLC-MS based methods for nicotine and/or cotinine analysis in various biological matrices. The sample preparation, mass and chromatographic conditions and method validation results of these methods have been summarized and analyzed. Sample was mainly pretreated by protein precipitation and/or extraction. Separation was achieved using methanol and/or acetonitrile:water (with or without ammonium acetate) on C18 columns, and acetonitrile:water (with formic acid, ammonium acetate/formate) on HILIC columns. Nicotine-d3, nicotine-d4 and cotinine-d3 were commonly used internal standards. Other non-deuterated IS were also used such as ritonavir, N-ethylnorcotinine, and milrinone. For both nicotine and cotinine, the calibration range was 0.005-35000 ng/mL, the matrix effect was 75.96% - 126.8% and the recovery was 53% - 124.5%. The two analytes were stable at room temperature for 1-10 days, at -80 °C for up to 6 months, and after 3-6 freeze-thaw cycles. Comedications did not affect nicotine and cotinine analysis.
The composition of the gut microbiome in patients with sarcopenia

Abstract Objectives The purpose of this study is to predict sarcopenia by analyzing the composition of the gut microbiota. Methods We collected fecal samples for 16S rRNA sequencing, then we used the data results to analyze the diversity and composition of the gut microbiota and calculated the relationship between biochemical indexes and the microbiota. Results According to PCA and heatmap analysis, the characteristics of patients could be divided into two categories. Moreover, the P/B (Prevotella/Bacteroides) ratio of the sarcopenia group was higher than that of the control group in terms of relative abundance. A box plot based on the Chao1 and observed OTU values indicated both the relative abundance and diversity of the gut microbiota in sarcopenia patients were lower than those in the control group. After we applied binary logistic regression and ROC curve analysis to the data, we confirmed that three indexes (P/B value, Coprococcus, and Lachnospiraceae) could be used to predict sarcopenia. Conclusions We can distinguish sarcopenia patients through the gut microbiota P/B index (over 1.7), the relative amount of Coprococcus (1.00–3.70%), and the relative amount of Lachnospiraceae (0.00–1.68%). Sarcopenia can be predicted with the help of the gut micro-community, which provides an improvement in methodology.
Far-field optical imaging of topological edge states in zigzag plasmonic chains

Abstract Topological photonics mimicking topological insulators has recently attracted considerable attention. The Su–Schrieffer–Heeger (SSH) model, which is a fundamental topological system, has been experimentally demonstrated in many photonic systems owing to its simplicity. In particular, a zigzag chain, which is described by the SSH model, shows intriguing functionality such as polarization-dependent switching of topological edge states. To date, the far-field imaging of topological edge states in plasmonic chains has not been reported because of the constraint imposed by the diffraction limit. In this study, we experimentally observed the photonic topological edge states of zigzag plasmonic chains composed of metal nanodiscs in the optical region through far-field imaging. Using a chain longer than the diffraction limit, light scattering from the two edges of the zigzag chains was resolved. In the case of such a long chain, it was revealed that tiny gaps of several nanometers between the discs, which are difficult to fabricate, are necessary. Therefore, we propose connected chains and investigate the effect of the shape of the connected part, which reveals that similar topological edge states can be obtained even in the connected chains. The polarization dependence of edge-state imaging showed switching of the systems in trivial and topological phases in the same zigzag chain. Far-field observations serve as an easy and effective tool for the investigation and application of photonic topological edge states.
Workplace Training and Human Capital: Livelihood Protection and Promotion in Urban China

Workplace training produces 2 types of human capital: general and firm-specific. Based on specific human capital theories pioneered by Gary Becker, this article empirically examines the impact of on-the-job training and off-the-job training on wage levels in urban China. It is found that off-the-job training in previous firms significantly raises wages at a worker's current firm, whereas previous on-the-job training has no effect on current wages. The results are consistent with theory and U.S. experience. The results are robust to various specifications and procedures correcting for potential error clustering and selection bias problems. It is suggested that advocating firm and government cosponsored general training programs targeting disadvantaged urban populations is a desirable and feasible strategy in an attempt to relieve the increasing unemployment pressure in China.
Teachers’ Perceptions of Their Jobs: A Multilevel Analysis of the Teacher Foliow-Up Survey for 1994—95

This study examined teachers’ perceptions of their jobs and teacher turnover through an analysis of data from the National Center for Education Statistics Schools and Staffing Survey and Teacher Follow-Up Survey. Our analysis suggests that student discipline problems were a major reason for teachers’ dissatisfaction with their jobs, second only to low compensation. Private school teachers generally encountered fewer student discipline problems and perceived their professional lives more favorably than public school teachers, although private schools usually offer lower salaries than public schools. Minority teachers were less satisfied with work conditions and student discipline problems than nonminority teachers. These findings imply policy changes for teacher retention.