Miracle-dz/UniFAR-FTUs huggingface dataset:
Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif

Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its target genes have inherent asymmetry in regulation, even when their promoters are identical; the TF gene being more repressed than its targets. The magnitude of asymmetry depends on network features such as network size and TF-binding affinities. Intriguingly, asymmetry disappears when the growth rate is too fast or too slow and is most significant for typical growth conditions. These results highlight the importance of accounting for network architecture in quantitative models of gene expression.
Smartphone and Mobile Health Apps for Tinnitus: Systematic Identification, Analysis, and Assessment

Background Modern smartphones contain sophisticated high-end hardware features, offering high computational capabilities at extremely manageable costs and have undoubtedly become an integral part in users' daily life. Additionally, smartphones offer a well-established ecosystem that is easily discoverable and accessible via the marketplaces of differing mobile platforms, thus encouraging the development of many smartphone apps. Such apps are not exclusively used for entertainment purposes but are also commonplace in health care and medical use. A variety of those health and medical apps exist within the context of tinnitus, a phantom sound perception in the absence of any physical external source. Objective In this paper, we shed light on existing smartphone apps addressing tinnitus by providing an up-to-date overview. Methods Based on PRISMA guidelines, we systematically searched and identified existing smartphone apps on the most prominent app markets, namely Google Play Store and Apple App Store. In addition, we applied the Mobile App Rating Scale (MARS) to evaluate and assess the apps in terms of their general quality and in-depth user experience. Results Our systematic search and screening of smartphone apps yielded a total of 34 apps (34 Android apps, 26 iOS apps). The mean MARS scores (out of 5) ranged between 2.65-4.60. The Tinnitus Peace smartphone app had the lowest score (mean 2.65, SD 0.20), and Sanvello—Stress and Anxiety Help had the highest MARS score (mean 4.60, SD 0.10). The interrater agreement was substantial (Fleiss κ=0.74), the internal consistency was excellent (Cronbach α=.95), and the interrater reliability was found to be both high and excellent—Guttman λ6=0.94 and intraclass correlation, ICC(2,k) 0.94 (95% CI 0.91-0.97), respectively. Conclusions This work demonstrated that there exists a plethora of smartphone apps for tinnitus. All of the apps received MARS scores higher than 2, suggesting that they all have some technical functional value. However, nearly all identified apps were lacking in terms of scientific evidence, suggesting the need for stringent clinical validation of smartphone apps in future. To the best of our knowledge, this work is the first to systematically identify and evaluate smartphone apps within the context of tinnitus.
Antibiotic Prophylaxis for Thyroid and Parathyroid Surgery: A Systematic Review and Meta-analysis

Objective Although thyroid and parathyroid surgery is considered a clean procedure with a low incidence of surgical site infections (SSIs), a great number of endocrine surgeons use antibiotic prophylaxis (AP). The aim of this study was to assess whether AP is significantly effective in reducing the incidence of SSIs in this kind of surgery. Data Sources A systematic literature search was performed with PubMed, Scopus, and ISI–Web of Science. Studies addressing the efficacy of AP in reducing the incidence of SSIs in thyroid and parathyroid surgery were included in the systematic review and meta-analysis. Review Methods The random effects model was assumed to account for different sources of variation among studies. The overall effect size was computed through the inverse variance method. Heterogeneity across studies, possible outlier studies, and publication bias were evaluated. Results A total of 6 studies with 4428 patients were included in the quantitative analysis. The incidence of SSI was 0.6% in the case group and 0.4% in the control group (odds ratio, 1.07; 95% CI, 0.3-3.81; P = .915). There was no evidence of heterogeneity among the studies (Q = 8.36, P = .138; I2 = 40.17). The analysis of several continuous moderators, including age, use of drain, and duration of surgery, did not generate any significant result. Conclusion AP is not effective in reducing the incidence of SSI in thyroid and parathyroid surgery and should be avoided, notwithstanding the negative impact on social costs and the risk of development of antibiotic resistance.
Accelerometer Measurements Indicate That Arm Movements of Children With Cerebral Palsy Do Not Increase After Constraint-Induced Movement Therapy (CIMT).

IMPORTANCE Constraint-induced movement therapy (CIMT) is a common treatment for children with unilateral cerebral palsy (CP). Although clinic-based assessments have demonstrated improvements in arm function after CIMT, whether these changes are translated and sustained outside of a clinic setting remains unclear. OBJECTIVE Accelerometers were used to quantify arm movement for children with CP 1 wk before, during, and 4 wk or more after CIMT; measurements were compared with those from typically developing (TD) peers. DESIGN Observational. SETTING Tertiary hospital and community. PARTICIPANTS Seven children with CP (5 boys, 2 girls; average [AVE] age ± standard deviation [SD] = 7.4 ± 1.2 yr) and 7 TD peers (2 boys, 5 girls; AVE age ± SD = 7.0 ± 2.3 yr). INTERVENTION 30-hr CIMT protocol. OUTCOMES AND MEASURES Use ratio, magnitude ratio, and bilateral magnitude were calculated from the accelerometer data. Clinical measures were administered before and after CIMT, and parent surveys assessed parent and child perceptions of wearing accelerometers. RESULTS During CIMT, the frequency and magnitude of paretic arm use among children with CP increased in the clinic and in daily life. After CIMT, although clinical scores showed sustained improvement, the children's accelerometry data reverted to baseline values. Children and parents in both cohorts had positive perceptions of accelerometer use. CONCLUSIONS AND RELEVANCE The lack of sustained improvement in accelerometry metrics after CIMT suggests that therapy gains did not translate to increased movement outside the clinic. Additional therapy may be needed to help transfer gains outside the clinic. WHAT THIS ARTICLE ADDS Accelerometer measurements were effective at monitoring arm movement outside of the clinic during CIMT and suggested that additional interventions may be needed after CIMT to sustain benefits.
Job Insecurity, Sickness Presenteeism and the Moderating Effect of Workplace Health Promotion.

OBJECTIVE This study examined the relationship between job insecurity and presenteeism, and the role of workplace health promotion as moderator in this association. METHODS We used data from 9,525 employees from the 6 BIBB/BAuA Employment Survey 2012 for the working population in Germany. Data analysis was performed with logistic regressions. RESULTS Job insecurity was associated with a higher risk of presenteeism, even after adjustment for control factors (OR = 1.25, CI: 1.01-1.53, p < 0.05). Workplace health promotion moderated this relationship: It no longer existed in companies with health promotion. CONCLUSIONS The results suggest that employees with job insecurity are more likely to work despite feeling ill with the aim of securing their jobs. By establishing workplace health promotion, companies can protect their employees from that behavior in order to avoid negative long-term consequences.
Rehabilitation Exergames: Use of Motion Sensing and Machine Learning to Quantify Exercise Performance in Healthy Volunteers

Background Performing physiotherapy exercises in front of a physiotherapist yields qualitative assessment notes and immediate feedback. However, practicing the exercises at home lacks feedback on how well patients are performing the prescribed tasks. The absence of proper feedback might result in patients performing the exercises incorrectly, which could worsen their condition. We present an approach to generate performance scores to enable tracking the progress by both the patient at home and the physiotherapist in the clinic. Objective This study aims to propose the use of 2 machine learning algorithms, dynamic time warping (DTW) and hidden Markov model (HMM), to quantitatively assess the patient’s performance with respect to a reference. Methods Movement data were recorded using a motion sensor (Kinect V2), capable of detecting 25 joints in the human skeleton model, and were compared with those of a reference. A total of 16 participants were recruited to perform 4 different exercises: shoulder abduction, hip abduction, lunge, and sit-to-stand exercises. Their performance was compared with that of a physiotherapist as a reference. Results Both algorithms showed a similar trend in assessing participant performance. However, their sensitivity levels were different. Although DTW was more sensitive to small changes, HMM captured a general view of the performance, being less sensitive to the details. Conclusions The chosen algorithms demonstrated their capacity to objectively assess the performance of physical therapy. HMM may be more suitable in the early stages of a physiotherapy program to capture and report general performance, whereas DTW could be used later to focus on the details. The scores enable the patient to monitor their daily performance. They can also be reported back to the physiotherapist to track and assess patient progress, provide feedback, and adjust the exercise program if needed.
Wnts regulate planar cell polarity via heterotrimeric G protein and PI3K signaling

The planar cell polarity (PCP) pathway is essential for tissue morphogenesis. However, the roles of Wnt ligands in the mammalian PCP pathway remain poorly understood. This study identifies a Wnt/heterotrimeric G protein/PI3K pathway that regulates cell-intrinsic and tissue-level PCP in the mouse cochlea.
Long-term high-concentrate diet feeding induces apoptosis of rumen epithelial cells and inflammation of rumen epithelium in dairy cows

Abstract The aim of the present study was to evaluate how long-term high-concentrate diet feeding affected rumen epithelium (RE) of dairy cows. So, 12 mid-lactating multiparous cows were divided into two groups randomly fed either with high-concentrate diet (HC, concentrate: forage = 6: 4) or low-concentrate diet (LC, concentrate: forage = 4:6) for 20 weeks. Remarkable upregulation of lipopolysaccharide (LPS) level and depress of pH in rumen fluid were induced by HC compared with LC group. mRNA abundance of interleukin-6 (IL-6), interleukin-8 (IL-8), C-C motif chemokine ligand 5 (CCL5), caspase-3, caspase-8, and caspase-9 were elevated in RE of HC group compared with LC group. Greater protein abundance of phosphorylated NF-κB p65, IL-6, and tumor necrosis factor α (TNF-α) was observed in RE of cows fed HC than that fed LC. Abundance of protein related to proapoptotic response (cytochrome c, BAX and caspase-3) in HC group was greater than that in LC group, while the abundance of anti-apoptotic factor protein (Bcl-2) was lower in HC group than LC group. Therefore, the present study demonstrated that long-term high-concentrate diet feeding upregulated LPS level in rumen fluid and induced the proinflammatory response in the rumen epithelium and apoptosis of rumen epithelial cells.
PROJETO TRILHA SUBAQUÁTICA: SUGESTÃO DE DIRETRIZES PARA A CRIAÇÃO DE MODELOS DE EDUCAÇÃO AMBIENTAL EM UNIDADES DE CONSERVAÇÃO LIGADAS A ECOSSISTEMAS MARINHOS

A educacao ambiental (EA) embasa acoes de ecoturismo e recreacao, instrumentos pro-ativos na gestao de UCs, incluidos dentro de uma de suas atividades-fim, o uso publico. Entretanto, para que sejam atingidos os objetivos previstos, e necessario que as atividades de (EA) sejam conceitualmente e operacionalmente bem estruturadas, dentro de modelos educacionais definidos e testados. Mundialmente, atividades de educacao ambiental (EA) marinha sao raras e criacao de modelos e de grande importância no incentivo a sua implementacao em UCs marinhas ou que tenham seu entorno atingindo esse ambiente. O presente trabalho descreve e avalia os 7 modelos do Projeto Trilha Subaquatica, criado em 2002, como atividade de EA e extensao universitaria: Trilha Subaquatica (TS) em mergulho livre; TS em mergulho autonomo, Palestra, Aquario Natural, Trilha em Caiaques no Manguezal, Trilha Geologica e TS Virtual. Os modelos foram baseados em um conceito de EA holistica, transformadora e multidisciplinar, com abordagem de trilha interpretativa guiada. Entre 2002 e 2006 foram realizadas 5598 atividades, com um numero maximo de visitantes em 2004, totalizando 3776 atividades, 2624 ligadas a visitacao publica. Entre 2003 e 2004 ao redor de 2000 atividades foram realizadas envolvendo professores e alunos de escolas publicas de Ubatuba, resultando no treinamento de 51 professores. No geral, um impacto emocional intenso foi observado na maioria dos praticantes e o ganho de conhecimentos foi grande. O conjunto de modelos mostrou-se adequado a diferentes perfis de interesses, faixas etarias e niveis de escolaridade. Entretanto, o principal produto do projeto foi a formacao, entre 2002 e 2007, de 108 monitores, dos quais 40% permaneceram no projeto por um ou mais anos consecutivos, auxiliando no treinamento dos novos e servindo como agentes multiplicadores. A selecao desses profissionais por gestores de UCs de forma a que possam implementar seu proprio projeto pode ser feita no site www.ib. usp.br/ecosteiros.
Histone deacetylase inhibitors in myeloproliferative neoplasms: current roles and future prospects

ABSTRACT Introduction: Enhanced understanding of the pathogenesis of Myeloproliferative Neoplasms (MPN) has led to the rapid introduction of novel therapeutic agents into clinical practice. Knowledge of the genetic landscape (eg. JAK2, MPL and CALR as commonly mutated genes) is increasing and has been used to model novel, effective therapies. Histone Deacetylases (HDAC) are heavily involved in epigenetic modulation; their aberrant expression has been demonstrated, both in vitro and in vivo, in various MPN. A number of HDAC inhibitors (HDACi) have since been developed with the aim to reverse this epigenetic dysregulation. Areas covered: The role of HDACi in MPN is reviewed in detail in addition to an update on the currently available clinical trial information. It is of pivotal importance to understand how these agents fit into the current therapeutic strategy for management of MPN. Expert opinion: HDACi certainly have a role in the management of MPN but clarification on the dosing and scheduling is required. Moreover, whether these agents should be used sequentially to agents such as JAK inhibitors or in combination is an area of active investigation.
Interaction between Marbofloxacin and Flunixin in Treatment of Pneumonia in Lambs

Nasopharyngeal swabs were collected from 100 lambs aging 9 -12 months (30 healthy and 70 pneumonic lambs for bacteriological examination. Overall, 25% were positive for P multocida. Antibiogram study of the isolates revealed that marbofloxacin was the highest effective against P. multocida. Forty lambs (20 healthy and 20 naturally infected with P multocida) were divided into 8 groups (5, each), the 1 st group: healthy lambs (control), 2 nd group: healthy received marbofloxacin, 3 rd group: healthy received flunixin meglumine, 4 th group: healthy received marbofloxacin and flunixin meglumine together, 5 th group: infected non treated, 6 th group: infected treated with marbofloxacin, 7 th group: infected treated with flunixin meglumine and 8 th : group infected treated with marbofloxacin and flunixin meglumine together. Hematobiochemical changes at 1 st , 7 th and 14 th day post treatment were studied. All clinical sign disappeared and P.multocida microorganisms were not reisolated in group post treated by marbofloxacin alone or together with flunixin meglumine. Healthy lambs received marbofloxacin or flunixin meglumine either alone or together showed significant decrease in RBCs, Hb, PCV%, T protein, albumin, globulin, α, β, γ globulin and significant increase in WBCs, AST, ALT, ALP, GGT, urea and creatinine at1 st and 7 th day post injection. Pneumonic lambs showed significant reduction in RBCs, Hb, PCV% T. protein, albumin, total globulin, α, β globulin and significant increase in WBCs, AST, ALT, ALP, GGT, γ globulin, urea and creatinine all over the experimental period. Pneumonic lamb treated with marbofloxacin alone or with flunixin meglumine resulted in complete disappearance of these clinical signs at 1 st day post treatment but these clinical signs remained in flunixin meglumine alone lambs. It is concluded that, pasteurellosis in lambs resulted in adverse effect in hematobiochemical parameters. Using marbofloxacin alone or together with flunixin meglumine in treatment of diseased lambs lead to improve clinical signs and hemato-biochemical parameters at 7 th day post treatment.
4HNE Impairs Myocardial Bioenergetics in Congenital Heart Disease-Induced Right Ventricular Failure

Supplemental Digital Content is available in the text. Background: In patients with complex congenital heart disease, such as those with tetralogy of Fallot, the right ventricle (RV) is subject to pressure overload stress, leading to RV hypertrophy and eventually RV failure. The role of lipid peroxidation, a potent form of oxidative stress, in mediating RV hypertrophy and failure in congenital heart disease is unknown. Methods: Lipid peroxidation and mitochondrial function and structure were assessed in right ventricle (RV) myocardium collected from patients with RV hypertrophy with normal RV systolic function (RV fractional area change, 47.3±3.8%) and in patients with RV failure showing decreased RV systolic function (RV fractional area change, 26.6±3.1%). The mechanism of the effect of lipid peroxidation, mediated by 4-hydroxynonenal ([4HNE] a byproduct of lipid peroxidation) on mitochondrial function and structure was assessed in HL1 murine cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes. Results: RV failure was characterized by an increase in 4HNE adduction of metabolic and mitochondrial proteins (16 of 27 identified proteins), in particular electron transport chain proteins. Sarcomeric (myosin) and cytoskeletal proteins (desmin, tubulin) also underwent 4HNE adduction. RV failure showed lower oxidative phosphorylation (moderate RV hypertrophy, 287.6±19.75 versus RV failure, 137.8±11.57 pmol/[sec×mL]; P=0.0004), and mitochondrial structural damage. Using a cell model, we show that 4HNE decreases cell number and oxidative phosphorylation (control, 388.1±23.54 versus 4HNE, 143.7±11.64 pmol/[sec×mL]; P<0.0001). Carvedilol, a known antioxidant did not decrease 4HNE adduction of metabolic and mitochondrial proteins and did not improve oxidative phosphorylation. Conclusions: Metabolic, mitochondrial, sarcomeric, and cytoskeletal proteins are susceptible to 4HNE-adduction in patients with RV failure. 4HNE decreases mitochondrial oxygen consumption by inhibiting electron transport chain complexes. Carvedilol did not improve the 4HNE-mediated decrease in oxygen consumption. Strategies to decrease lipid peroxidation could improve mitochondrial energy generation and cardiomyocyte survival and improve RV failure in patients with congenital heart disease.
Characterization of Whey-Based Fermented Beverages Supplemented with Hydrolyzed Collagen: Antioxidant Activity and Bioavailability

In this study, the preparation of a milk whey-based beverage with the addition of different concentrations of hydrolyzed collagen (0.3%, 0.5%, 0.75%, and 1%) was carried out. The control was considered at a concentration of 0%. Physicochemical properties, viscosity, antioxidant activity, and microbiological parameters were evaluated. The 1% collagen treatment showed the highest protein content (9.75 ± 0.20 g/L), as well as radical inhibition for ATBS (48.30%) and DPPH (30.06%). There were no significant differences (p ≥ 0.05) in the fat and lactose parameters. However, the pH in the control treatment was lower compared to beverages treated with hydrolyzed collagen. Fourier transform-infrared spectroscopy showed spectra characteristic of lactose and collagen amides. The viscosity increased significantly as the concentration of hydrolyzed collagen increased. The addition of hydrolyzed collagen increased the bioavailability, nutritional value, and the antioxidant activity of the beverage. Hydrolyzed collagen acted as an antimicrobial agent, as there was no presence of microorganism pathogens observed in the treated beverages.
What is the molecular basis of nonhost resistance?

Nonhost resistance is typically considered the ability of a plant species to repel all attempts of a pathogen species to colonize it and reproduce on it. Based on this common definition, nonhost resistance is presumed to be very durable and thus of great interest for its potential use in agriculture. Despite considerable research efforts, the molecular basis of this type of plant immunity remains nebulous. We here stress the fact that "nonhost resistance" is a phenomenological rather than a mechanistic concept that comprises more facets than typically considered. We further argue that nonhost resistance essentially relies on the very same genes and pathways as other types of plant immunity, of which some may act as bottlenecks for particular pathogens on a given plant species and/or under certain conditions. The frequently used term "nonhost genes" is thus misleading and should be avoided in our view. Depending on the plant-pathogen combination, nonhost resistance may involve the recognition of pathogen effectors by host immune sensor proteins, which might give rise to host shifts or host range expansions due to evolutionary-conditioned gains and losses in respective armories. The extent of nonhost resistance thus also defines pathogen host ranges. In some instances, immune-related genes can be transferred across plant species to boost defense, resulting in augmented disease resistance. We discuss future routes for deepening our understanding of nonhost resistance and argue that the confusing term "nonhost resistance" should be used more cautiously in the light of a holistic view on plant immunity.
Performance of a pre‐procedural Mehran score to predict acute kidney injury after percutaneous coronary intervention

Acute kidney injury (AKI) is a known complication of patients undergoing cardiac catheterization or percutaneous coronary interventions (PCI). The Mehran score was developed to identify patients at risk for AKI after cardiac catheterization or PCI, but its use of contrast volume as part of the score calculation limits its application prior to the procedure. In this study, we evaluated the utility of a modified Mehran score that utilizes only pre‐procedural data by excluding contrast volume.