Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes

Significance Time-series transcriptomes of a biological process are useful for identifying the regulators of the process. To analyze such data, we developed a method that avoids time-point alignment and normalization between two conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light–dark cycles and under total darkness and obtained a time-ordered gene coexpression network (TO-GCN) that likely includes all genes involved in the development of Kranz anatomy, a structure crucial for the high efficiency of C4 photosynthesis. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade of Kranz anatomy development. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of C4 enzyme genes, demonstrating its broad utility. Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light–dark cycles and under total darkness and obtained eight time-ordered gene coexpression networks (TO-GCNs), which can be used to predict upstream regulators of any genes in the GCNs. One of the eight TO-GCNs is light-independent and likely includes all genes involved in the development of Kranz anatomy, which is a structure crucial for the high efficiency of photosynthesis in C4 plants. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade upstream of SHORTROOT1, a key Kranz anatomy regulator. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of maize C4 enzyme genes and RUBISCO SMALL SUBUNIT2. Our study provides not only a powerful method but also novel insights into the regulatory networks underlying Kranz anatomy development and C4 photosynthesis.
The Performance of Fixed-Horizon, Look-Ahead Procedures Compared to Backward Induction in Bayesian Adaptive-Randomization Decision-Theoretic Clinical Trial Design

Abstract Designing optimal, Bayesian decision-theoretic trials has traditionally required the use of computationally-intensive backward induction. While methods for addressing this barrier have been put forward, few are both computationally tractable and non-myopic, with applications of the Gittins index being one notable example. Here we explore the look-ahead approach with adaptive-randomization, with designs ranging from the fully myopic to the fully informed. We compare the operating characteristics of the look-ahead designed trials, in which decision rules are based on a fixed number of future blocks, with those of trials designed using traditional backward induction. The less-myopic designs performed well. As the designs become more myopic or the trials longer, there were disparities in regions of the decision space that are transition zones between continuation and stopping decisions. The more myopic trials generally suffered from early stopping as compared to the less myopic and backward induction trials. Myopic trials with adaptive randomization also saw as many as 28 % of their continuation decisions change to a different randomization ratio as compared to the backward induction designs. Finally, early stages of myopic-designed trials may have disproportionate effect on trial characteristics.
Biofunctionalization of magnetite nanoparticles with stevioside: effect on the size and thermal behaviour for use in hyperthermia applications

Abstract Controlling the magnetic properties of a nanoparticle efficiently via its particle size to achieve optimized heat under alternating magnetic field is the central point for magnetic hyperthermia-mediated cancer therapy (MHCT). Here, we have shown the successful use of stevioside (a natural plant-based glycoside) as a promising biosurfactant to control the magnetic properties of Fe3O4 nanoparticles by controlling the particle size. The biocompatibility and cellular uptake efficiency by rat C6 glioma cells and calorimetric magnetic hyperthermia profile of the nanoparticles were further examined. Our finding suggests superior properties of stevioside-coated magnetite nanoparticles in comparison to polysorbate-80 and oleic acid coated nanomagnets as far as particle size reduction, biocompatibility, hyperthermic effect, and cellular uptake by the glioblastoma cancer cells are concerned. The stevioside-coated nanomagnets exhibiting the maximum temperature rise were further investigated as heating agents in in vitro magnetic hyperthermia experiments (405 kHz, 168 Oe), showing their efficacy to induce cell death of rat C6 glioma cells after 30 min at a target temperature T = 43 °C.
“It’s When the Trees Blossom”: Explanatory Beliefs, Stigma, and Mental Illness in the Context of HIV in Botswana

Mental illness is a common comorbidity of HIV and complicates treatment. In Botswana, stigma impedes treatment of mental illness. We examined explanatory beliefs about mental illness, stigma, and interactions between HIV and mental illness among 42 adults, from HIV clinic and community settings, via thematic analysis of interviews. Respondents endorse witchcraft as a predominant causal belief, in addition to drug abuse and effects of HIV. Respondents describe mental illness as occurring “when the trees blossom,” underscoring a conceptualization of it as seasonal, chronic, and often incurable and as worse than HIV. Consequently, people experiencing mental illness (PEMI) are stereotyped as dangerous, untrustworthy, and cognitively impaired and discriminated against in the workplace, relationships, and sexually, increasing vulnerability to HIV. Clinical services that address local beliefs and unique vulnerabilities of PEMI to HIV, integration with peer support and traditional healers, and rehabilitation may best address the syndemic by facilitating culturally consistent recovery-oriented care.
Effects of Equal Volume But Different Plyometric Jump Training Intensities on Components of Physical Fitness in Physically Active Young Males

Abstract Ramirez-Campillo, R, Moran, J, Drury, B, Williams, M, Keogh, JW, Chaabene, H, and Granacher, U. Effects of equal volume but different plyometric jump training intensities on components of physical fitness in physically active young males. J Strength Cond Res 35(7): 1916–1923, 2021—An 8-week single-blind randomized controlled trial was conducted to compare the effects of separate programs of equal volume, but different intensity, plyometric jump training (PJT), on physical fitness in healthy adults. Thirty-eight physically active males (mean age: 21.8 ± 2.5 years) participated. Subjects were randomly assigned to one of 3 PJT groups or a control (CON, n = 9) according to their jump performance. Plyometric jump training was conducted at maximal (PJT-100, n = 10), high (PJT-80, n = 9), or moderate (PJT-65, n = 10) intensity within each group. Baseline and follow-up tests were performed for the assessment of countermovement jump (CMJ) height, CMJ height with arm swing (CMJA), and drop jump height from a 20-cm drop box (DJ20), linear speed (30 m), and change-of-direction speed (CODS) (the Illinois CODS test). Results revealed significant group × time interactions for CMJ, CMJA, DJ20, 30-m sprint, and CODS (all p < 0.001; d = 0.39–0.76). Post hoc analyses showed significant improvements in all 5 fitness measures for PJT-100 (all p < 0.01, Δ3.7–13.5%, d = 0.26–1.4). For PJT-80, 3 of 5 fitness tests demonstrated significant change (CMJ: p < 0.001, Δ5.9%, d = 0.33; CMJA: p < 0.001, Δ7.0%, d = 0.43; CODS: p < 0.001, Δ3.9%, d = 0.9), and for PJT-65, only 1 test was significant (CMJ: p < 0.05, Δ2.8%, d = 0.15). No significant changes were observed in CON. Except for similar gains in DJ20 and 30-m sprint in PJT-100 and PJT-80, gains in physical fitness were, in general, greater (p < 0.05) after PJT-100 vs. PJT-80 vs. PJT-65 vs. CON. Therefore, maximal PJT intensity may induce larger physical fitness gains, although high and moderate intensities may also be useful, but to a lesser extent.
Dynamics of motor cortical activity during naturalistic feeding behavior

Objective. The orofacial primary motor cortex (MIo) plays a critical role in controlling tongue and jaw movements during oral motor functions, such as chewing, swallowing and speech. However, the neural mechanisms of MIo during naturalistic feeding are still poorly understood. There is a strong need for a systematic study of motor cortical dynamics during feeding behavior. Approach. To investigate the neural dynamics and variability of MIo neuronal activity during naturalistic feeding, we used chronically implanted micro-electrode arrays to simultaneously recorded ensembles of neuronal activity in the MIo of two monkeys (Macaca mulatta) while eating various types of food. We developed a Bayesian nonparametric latent variable model to reveal latent structures of neuronal population activity of the MIo and identify the complex mapping between MIo ensemble spike activity and high-dimensional kinematics. Main results. Rhythmic neuronal firing patterns and oscillatory dynamics are evident in single-unit activity. At the population level, we uncovered the neural dynamics of rhythmic chewing, and quantified the neural variability at multiple timescales (complete feeding sequences, chewing sequence stages, chewing gape cycle phases) across food types. Our approach accommodates time-warping of chewing sequences and automatic model selection, and maps the latent states to chewing behaviors at fine timescales. Significance. Our work shows that neural representations of MIo ensembles display spatiotemporal patterns in chewing gape cycles at different chew sequence stages, and these patterns vary in a stage-dependent manner. Unsupervised learning and decoding analysis may reveal the link between complex MIo spatiotemporal patterns and chewing kinematics.
In vivo Evidence of Cross-Reactivity between Cow’s Milk and Soybean Proteins in a Mouse Model of Food Allergy

Background: Cow’s milk allergy (CMA) is an important problem worldwide and the development of an in vivo system to study new immunotherapeutic strategies is of interest. Intolerance to soybean formula has been described in CMA patients, but it is not fully understood. In this work, we used a food allergy model in BALB/c mice to study the cross-reactivity between cow’s milk protein (CMP) and soy proteins (SP). Methods: Mice were orally sensitized with cholera toxin and CMP, and then challenged with CMP or SP to induce allergy. Elicited symptoms, plasma histamine, humoral and cellular immune response were analyzed. Th1- and Th2-associated cytokines and transcription factors were assessed at mucosal sites and in splenocytes. Cutaneous tests were also performed. Results: We found that the immediate symptoms elicited in CMP-sensitized mice orally challenged with SP were consistent with a plasma histamine increase. The serum levels of CMP-specific IgE and IgG1 antibodies were increased. These antibodies also recognized soy proteins. Splenocytes and mesenteric lymph node cells incubated with CMP or SP secreted IL-5 and IL-13. mRNA expression of Th2-associated genes (IL-5, IL-13, and GATA-3) was upregulated in mucosal samples. In addition, sensitized animals exhibited positive cutaneous tests after the injection of CMP or SP. Conclusions: We demonstrate that CMP-sensitized mice, without previous exposure to soy proteins, elicited hypersensitivity signs immediately after the oral administration of SP, suggesting that the immunochemical cross-reactivity might be clinically relevant. This model may provide an approach to further characterize cross-allergenicity phenomena and develop new immunotherapeutic treatments for allergic patients.
Clinical and Organizational Content of Clinical Pathways for Digestive Surgery: A Systematic Review

Background/Aims: Oncology surgery of the gastrointestinal tract is complex and infamous for its high complication rates. One of the methods for implementing interventions to optimize the patients’ condition and to enhance postoperative outcome is the development and implementation of a clinical pathway. The aim of this study was to analyze the content, i.e. the interventions of clinical pathways for digestive surgery and their effects on postoperative outcome measures. Methods: We performed a systematic review to study clinical pathways in hospital care for adult patients undergoing elective surgery of the stomach, esophagus, pancreas, liver, colon or rectum. The MEDLINE, EMBASE and CINAHL literature databases were searched. Results: The most common interventions in the clinical pathways in this review were defined in the pre- and postoperative phase and included: nutritional management, pain management, mobilization, education and discharge planning. The primary aim of these interventions was to enhance postoperative recovery. Conclusion: Clinical pathways for digestive surgery contain specific interventions to improve postoperative outcome. Most of these interventions are in accordance with the Enhanced Recovery After Surgery (ERAS) protocol, which is an evidence-based protocol for care after colon resections. They result in reduced length of stay without compromising other postoperative outcome measures.
Project GOLD: A pilot randomized controlled trial of a novel psychoeducational HIV/STI prevention intervention for heterosexually‐active black youth

Black youth account for the largest number of new HIV infections among heterosexual youth. Mental illness and difficulties in emotion regulation contribute to increased reports of HIV/sexually transmitted infection (STI) risk-related sexual behaviors in this group. Yet limited interventions exist to address this affective component of the sexual decision-making process. The purpose of this paper was to describe the trial design, research challenges, and baseline characteristics from a study designed to fill this gap. Project GOLD was a pilot randomized controlled trial of a psychoeducational HIV/STI prevention intervention designed to address the role of mental illness and emotion regulation in HIV/STI risk among heterosexually-active Black youth aged 14 to 17 (N = 108). Challenges encountered in the research process warrant further attention in future research (e.g., disagreement among the regulatory bodies on parental permission requirements). The most common mental health diagnoses were Recurrent Major Depressive Disorder (15.7%) and current substance abuse (7.4%). Participants reported higher levels of emotional suppression, and adaptive methods of emotion management, than culturally inappropriate expressions of anger or sadness. They also reported a mean age of 13.6 at first vaginal sex, used condoms 66% of the time for vaginal sex, and had an average of three sexual partners in the past 6 months. More than one-quarter (26.9%) had sex with more than one person in the same day. These findings indicate intervention is crucial for this population. The forthcoming trial evaluation will indicate the promise of such interventions in reducing HIV/STI infections in this key population.
Generation of pulmonary neuroendocrine cells and SCLC-like tumors from human embryonic stem cells

Cancer models based on cells derived from human embryonic stem cells (hESCs) may reveal why certain constellations of genetic changes drive carcinogenesis in specialized lineages. Here we demonstrate that inhibition of NOTCH signaling induces up to 10% of lung progenitor cells to form pulmonary neuroendocrine cells (PNECs), putative precursors to small cell lung cancers (SCLCs), and we can increase PNECs by reducing levels of retinoblastoma (RB) proteins with inhibitory RNA. Reducing levels of TP53 protein or expressing mutant KRAS or EGFR genes did not induce or expand PNECs, but tumors resembling early-stage SCLC grew in immunodeficient mice after subcutaneous injection of PNEC-containing cultures in which expression of both RB and TP53 was blocked. Single-cell RNA profiles of PNECs are heterogeneous; when RB levels are reduced, the profiles resemble those from early-stage SCLC; and when both RB and TP53 levels are reduced, the transcriptome is enriched with cell cycle–specific RNAs. Our findings suggest that genetic manipulation of hESC-derived pulmonary cells will enable studies of this recalcitrant cancer.
Effects of chronic exercise interventions on executive function among children and adolescents: a systematic review with meta-analysis

Objective To synthesise randomised controlled trials (RCTs) regarding the effects of chronic exercise interventions on different domain-specific executive functions (EFs) among children and adolescents. Design Systematic review with meta-analysis. Data sources PsycINFO, PubMed, SPORTDiscus, Academic Search Premier, Embase and Web of Science were searched. Eligibility criteria for selecting studies RCTs or cluster RCT design, which employ chronic exercise interventions and target healthy children (age 6–12 years) and adolescents (age 13–17 years). We defined chronic exercise as physical activity (PA) which consists of multiple exercise sessions per week and lasts for an extended period of time (typically over 6 weeks). Results We included 19 studies, with a total of 5038 participants. The results showed that chronic exercise interventions improved overall EFs (standardised mean difference (SMD)=0.20, 95% CI 0.09 to 0.30, p<0.05) and inhibitory control (SMD=0.26, 95% CI 0.08 to 0.45, P<0.05). In meta regression, higher body mass index was associated with greater improvements in overall EFs performance (β=0.03, 95% CI 0.0002 to 0.06, p<0.05), whereas age and exercise duration were not. In subgroup analysis by intervention modality, sports and PA programme (SMD=0.21, 95% CI 0.12 to 0.31, p<0.05) and curricular PA (SMD=0.39, 95% CI 0.08 to 0.69, p<0.05) improved overall EFs performance, but integrated PA did not (SMD=0.02, 95% CI −0.05 to 0.09, p>0.05). Interventions with a session length < 90 minutes improved overall EFs performance (SMD=0.24, 95%CI 0.10 to 0.39, p=0.02), but session length ≥ 90 minutes did not (SMD=0.05, 95%CI -0.03 to 0.14). No other moderator was found to have an effect. Conclusions Despite small effect sizes, chronic exercise interventions, implemented in curricular or sports and PA programme settings, might be a promising way to promote multiple aspects of executive functions, especially inhibitory control.
Recombinant production of active Streptococcus pneumoniae CysE in E. coli facilitated by codon optimized BL21(DE3)-RIL and detergent

Abstract The emergence of drug resistance in Streptococcus pneumoniae (Spn) is a global health threat and necessitates discovery of novel therapeutics. The serine acetyltransferase (also known as CysE) is an enzyme of cysteine biosynthesis pathway and is reported to be essential for the survival of several pathogenic bacteria. Therefore, it appears to be a very attractive target for structure–function understanding and inhibitor design. This study describes the molecular cloning of cysE from Spn in the pET21c vector and efforts carried out for expression and purification of active recombinant CysE. Significant expression of recombinant Spn cysE could be achieved in codon optimized BL21(DE3)-RIL strain as opposed to conventional BL21(DE3) strain. Analysis of codon adaptation index (CAI) with levels of eukaryotic genes and prokaryotic cysEs expressed in heterologous E. coli host suggests that codon optimized E. coli BL21(DE3)-RIL may be a better host for expressing genes with low CAI. Here, an efficient protocol has been developed for recovery of recombinant Spn CysE in soluble and biologically active form by the usage of nonionic detergent Triton X-100 at a concentration as low as 1%. Altogether, this study reports a simple strategy for producing functionally active Spn CysE in E. coli.
A Socio-Technical and Lean Approach Towards a Framework for Health Information Systems-Induced Error

The evaluation of Health Information Systems (HIS)-induced medication errors is crucial in efforts to understand its cause, impact and mitigation measures when trying to minimize errors and increase patient safety. A review of evaluation studies on HIS-induced medication errors was carried out, which indicated the need to further structure complex socio technical aspects of the subject. In order to satisfy this requirement, a new framework was introduced for the evaluation of HIS-induced error management in clinical settings. The proposed HO(P)T-fit framework (Human, Organization, Process and Technology-fit) was developed after critically appraising existing findings in HIS related evaluation studies. It also builds on previous models related to HIS evaluation, in particular, the HOT-fit (Human, Organization, Process and Technology-fit) framework, error model, business process management, Lean method, and medication workflow. HOPT-fit incorporates the concept of fit between the four factors. The framework has the potential to be used as a tool to conduct a structured, systematic, and comprehensive HIS evaluation.
Quantum-mechanical LSERs for the concentration-dependent adsorption of aromatic organic compounds by activated carbon: Applications and comparison with carbon nanotubes

ABSTRACT Carbon nanotubes (CNTs) have taken precedence over activated carbon in various applications where adsorption is the primary process. The adsorption of chemical compounds by CNTs and activated carbon is most often predicted through linear free energy/solvation energy relationships (LFERs/LSERs). This work proposes quantum-mechanical LSER models based on a combination of quantum-mechanical descriptors and solvatochromic descriptors of LSERs for predicting the adsorption of aromatic organic compounds by activated carbon at varying adsorbate concentrations. The models are validated using state-of-the-art procedures employing an external prediction set of compounds. This work reveals the hydrogen bond donating and accepting ability of compounds to be the most influencing – but a negative – factor in the adsorption process of activated carbon. The quantum-mechanical LSERs proposed in this work are analysed and found to be equally reliable as the existing LSERs. These were further used to predict the adsorption of nucleobases, steroid hormones, agrochemicals, endocrine disruptors and pharmaceutical drugs. Notably, agrochemicals and endocrine disruptors are predicted to be adsorbed more strongly by activated carbon when compared with their adsorption by CNTs. However, quantum-mechanical LSERs predict the adsorption strength of biomolecules on activated carbon to be similar to that on the CNTs, which can be used to assess the risk associated with using carbon materials.