Miracle-dz/UniFAR-FTUs huggingface dataset:
Antimicrobial resistance profiles of Streptococcus suis isolated from pigs, wild boars, and humans in France between 1994 and 2020

ABSTRACT Streptococcus suis, an emerging zoonotic pathogen, causes invasive infections and substantial economic losses in the pig industry worldwide. Antimicrobial resistance against 22 antibiotics was studied for 200 S. suis strains collected in different geographical regions of France. Most of the strains (86%) showed resistance to at least one antibiotic with a low rate of resistance to fluoroquinolones, penicillins, pleuromutilin, and diaminopyrimidine-sulfonamides, and a higher rate to macrolides-lincosamides and tetracycline. Multi-resistance patterns were observed in 138 strains; three of them being resistant to six antibiotic families. Statistical analyses highlighted a decrease in the resistance to trimethoprim-sulfamethoxazole, in our collection, between the two periods studied—before 2010 and after 2015—as well as an impact of the geographical origin with a higher rate of resistance to macrolides-lincosamides and penicillin in Brittany than in the other French regions. Furthermore, macrolides-lincosamides and tetracycline resistance patterns were more likely to be found in pig isolates than in human and wild boar isolates. A difference in resistance was also observed between serotypes. Most of the penicillin-resistant strains belong to serotypes 1, 5, 9, 11, 12, 15, 27, and 29. Finally, penicillin and pleuromutilin resistances were mostly found in “non-clinical” isolates. The empirical treatment of human and porcine infections due to S. suis in France can therefore still be carried out with beta-lactams. However, this study emphasizes the need to monitor antimicrobial resistance in this zoonotic pathogen.
A sampling theorem with error estimation for S-transform

ABSTRACT S-transform (ST) is an extension of wavelet transform (WT) and short-time Fourier transform (STFT). The ST is depended on a scalable and moving Gaussian window. It overcomes the low-resolution factor of STFT and tackles with a lack of phase in WT. The ST is a useful tool for signal processing and analysis. In this paper, the multiresolution analysis (MRA) related with ST is introduced and after that a sampling theorem associated with ST is proposed which is based on multiresolution subspace. Additionally, truncation and aliasing error generated due to the sampling process, are also derived. The theoretical determinations are exhibited and validated using simulation results.
Loke zupa decoction attenuates bronchial EMT-mediated airway remodelling in chronic asthma through the PI3K-Akt/HIF-1α signaling pathway

Abstract Context Loke zupa decoction (Lok) is a well-established classic Chinese folk remedy for asthma. Objective We sought to investigate the effect and mechanism of Lok on asthma airway remodelling and provide novel insights for the prevention and treatment of asthma. Materials and methods For in vitro experiments, BEAS-2B cells were assigned into six groups: Control, TGF-β1 (10 μM), TGF-β1 + Lok-20, TGF-β1 + Lok-40, TGF-β1 + Lok-80 μg/mL and TGF-β1 + SB431542 (5 μM). CCK8 and wound healing assays were performed. For in vivo experiments, 60 female BALB/c mice were randomly divided into 5 groups: Control, model, Lok-4.55, Lok-9.1, and DEX group. Lok was administrated by gavage during the challenge stage for 8 consecutive weeks (4.55 and 9.1 g/kg/day). We investigated airway inflammation and airway remodelling in the lungs and verified the activation status of EMT-related markers and the PI3K-Akt/HIF-1α signalling pathway. Results In vitro, Lok efficiently inhibited TGF-β1-induced BEAS-2B cell proliferation ability (cell viability 165% vs. 105%) and migration (migration areas 85% vs. 35%) without affecting their normal growth (IC50 274.2 µg/mL at 48 h). In vivo, Lok effectively protected mice from asthma, as evidenced by decreased histological damage and level of cytokines in BALF (IL-4, IL-13 and TGF-β1) by 17%–77%. Mechanistic research revealed that Lok reduced the levels of EMT-related molecules and significantly downregulated the PI3K-Akt/HIF-1α signalling pathway. Discussion and conclusions Our findings provide novel insights into the protective effect of Lok on asthma and the underlying mechanisms, providing a theoretical basis and potential treatment possibilities for this patient population.
cis-Decalin-containing tetramic acids as inhibitors of insect steroidogenic glutathione S-transferase Noppera-bo

Decalin-containing tetramic acid is a bioactive scaffold primarily produced by filamentous fungi. The structural diversity of this group of compounds is generated by characteristic enzymes of fungal biosynthetic pathways, including polyketide synthase/nonribosomal peptide synthetase hybrid enzymes and decalin synthase, which are responsible for the construction of a linear polyenoyl tetramic acid structure and stereoselective decalin formation via the intramolecular Diels–Alder reaction, respectively. Compounds that differed only in the decalin configuration were collected from genetically engineered mutants derived from decalin-containing tetramic acid-producing fungi and used for a structure-activity relationship study. Our evaluation of biological activities, such as cytotoxicity against several cancer cell lines and antibacterial, antifungal, antimalarial, and mitochondrial inhibitory activities, demonstrated that the activity for each assay varies depending on the decalin configurations. In addition to these known biological activities, we revealed that the compounds showed inhibitory activity against the insect steroidogenic glutathione S-transferase Noppera-bo. Engineering the decalin configurations would be useful not only to find derivatives with better biological activities but also to discover overlooked biological activities.
Overall and cause-specific mortality in patients with dementia: a population-based cohort study in Taiwan

OBJECTIVES OBJECTIVES: Information regarding the underlying causes of death (UCODs) and standardized mortality ratio (SMR) of dementia is instrumental in formulating medical strategies to prolong life in persons with dementia (PWD). We examined the leading UCODs among PWD and estimated the overall and cause-specific SMRs in relation to dementia in Taiwan. METHODS Data were retrieved from 2 national datasets: the Taiwan Death Registry and the medical claim datasets of the National Health Insurance program. The observed person-years for each study participant were counted from the date of cohort enrollment to either the date of death or the final day of 2016. Sex-specific and age-specific SMRs were then calculated. RESULTS The leading UCOD was circulatory disease, accounting for 26.0% of total deaths (n=3,505), followed by respiratory disease at 21.3% (n=2,875). PWD were at significantly increased risk of all-cause mortality (SMR, 2.01), with SMR decreasing with advancing age. A cause-specific analysis revealed that the highest SMRs were associated with nervous system diseases (SMR, 7.58) and mental, behavioral, and neurodevelopmental disorders (SMR, 4.80). Age appeared to modify SMR, suggesting that younger age at cohort enrollment was linked to higher SMRs for nearly all causes of mortality. CONCLUSIONS Circulatory and respiratory diseases were the leading UCODs among PWD. The particularly elevated mortality due to nervous system diseases and mental disorders suggests that allocating more resources to neurological and psychiatric services is warranted. The elevated SMRs of various UCODs among younger PWD underscore the need for clinicians to pay particular attention to the medical care provided to these patients.
EXPRESS: Reading(,) with and without commas.

All major writing systems mandate the use of commas to separate clauses and list items. However, casual writers often omit mandatory commas (Lunsford & Lunsford, 2008). Little empirical or theoretical research has been done on the effect that omitting mandatory commas has on eye movement control during reading. We present an eye-tracking experiment in Spanish, a language with a clear standard as to mandatory comma use. Sentences were presented with or without mandatory commas while readers' eye movements were recorded. There was a local increase in in go-past time for the pre-comma region when commas were presented, which was balanced out by shorter first-pass and second-pass times on the subsequent regions. In global sentence reading time, there was no evidence for an advantage of presenting commas. These findings suggest that, even when commas are mandatory, their effect is to shift when processing takes place rather than to facilitate processing overall.
Circulating microRNAs and cytokines as prognostic biomarkers for doxorubicin-induced cardiac injury and for evaluating the effectiveness of an exercise intervention.

PURPOSE To define a set of biomarkers that can be used to identify patients at high risk of developing late DOX-induced cardiac morbidity with the goal of focused monitoring and early interventions. EXPERIMENTAL DESIGN Mice received phosphate buffered saline or DOX 2.5 mg/kg 2x/week for 2 weeks. Blood samples were obtained before and after therapy for quantification of miRNAs (6 and 24 h), cytokines (24 h), and troponin (24 h, 4 and 6weeks). Cardiac function was evaluated using echocardiography before and 24 h after therapy. To assess the effectiveness of exercise intervention in preventing DOX-induced cardiotoxicity blood samples were collected from mice treated with DOX or DOX + exercise. Plasma samples from 13 DOX-treated sarcoma patients were also evaluated before and 24 h after therapy. RESULTS Elevations in in plasma miRNA-1, miRNA-499 and IL-1α, IL-1β, and IL-6 were seen in DOX-treated in mice with decreased ejection fraction and fractional shortening 24 h after DOX therapy. Troponin levels were not elevated until 4 weeks after therapy. In mice treated with exercise during Dox there was no elevation in these biomarkers and no change in cardiac function. Elevations in these biomarkers were seen in 12 of 13 sarcoma patients treated with Dox. CONCLUSIONS These findings define a potential set of biomarkers to identify and predict patients at risk for developing acute and late cardiovascular diseases with the goal of focused monitoring and early intervention. Further studies are needed to confirm the predictive value of these biomarkers in late cardiotoxicity.
Co‐chaperone BAG3 enters autophagic pathway via its interaction with microtubule associated protein 1 light chain 3 beta

The co‐chaperone BAG3 is a hub for a variety of cellular pathways via its multiple domains and its interaction with chaperones of the HSP70 family or small HSPs. During aging and under cellular stress conditions in particular, BAG3, together with molecular chaperones, ensures the sequestration of aggregated or aggregation‐prone ubiquitinated proteins to the autophagic‐lysosomal system via ubiquitin receptors. Accumulating evidence for BAG3‐mediated selective autophagy independent of cargo ubiquitination led to analyses predicting a direct interaction of BAG3 with LC3 proteins. Phylogenetically, BAG3 comprises several highly conserved potential LIRs, LC3‐interacting regions, which might allow for the direct targeting of BAG3 including its cargo to autophagosomes and drive their autophagic degradation. Based on pull‐down experiments, peptide arrays and proximity ligation assays, our results provide evidence of an interaction of BAG3 with LC3B. In addition, we could demonstrate that disabling all predicted LIRs abolished the inducibility of a colocalization of BAG3 with LC3B‐positive structures and resulted in a substantial decrease of BAG3 levels within purified native autophagic vesicles compared with wild‐type BAG3. These results suggest an autophagic targeting of BAG3 via interaction with LC3B. Therefore, we conclude that, in addition to being a key co‐chaperone to HSP70, BAG3 may also act as a cargo receptor for client proteins, which would significantly extend the role of BAG3 in selective macroautophagy and protein quality control.
Pediatric Hospitalizations at Rural and Urban Teaching and Nonteaching Hospitals in the US, 2009-2019

Key Points Question How have pediatric inpatient hospitalizations at US urban and rural general hospitals and freestanding children’s hospitals changed from 2009 to 2019? Findings In this cross-sectional analysis of a national data set representing an estimated 23.2 million inpatient pediatric hospitalizations from 2009 to 2019, birth hospitalizations decreased by 10.6%, whereas nonbirth hospitalizations decreased by 28.9%. The largest decreases were at urban nonteaching and rural hospitals, most of which had 25 or fewer nonbirth pediatric hospitalizations in 2019. Meaning These findings suggest that clinical and policy initiatives to support hospitals with low pediatric volumes may be needed to maintain pediatric hospital access and capabilities, particularly in rural communities.
Identifying the optimal cutoff point of Ki-67 in breast cancer: a single-center experience

Objective Ki-67 is associated with breast cancer subtypes, but the optimal cutoff point of Ki-67 has not been established in our center. We evaluated the cutoff point of Ki-67 in breast cancer and analyzed the associations among Ki-67, clinicopathological features, and prognosis. Methods The clinicopathological data and prognostic information of patients with breast cancer treated in our center were retrospectively collected, and the optimal cutoff point of Ki-67 was determined by univariate and multivariate survival risk analyses. The cutoff point was used to group the patients, and the differences in the clinicopathological features and prognosis were analyzed between the two groups. Results In total, 609 patients with estrogen receptor-positive and human epidermal growth factor receptor 2-negative primary breast cancer were enrolled. The mean Ki-67 value was 22.3% ± 15.4%, the median was 20%, and a cutoff point of 30% was an independent factor influencing recurrence-free survival. When 30% was used as the cutoff point, patients with a Ki-67 value of ≤30% had a better prognosis and lower tumor malignancy. Conclusion The optimal cutoff point of Ki-67 in breast cancer in our center is 30%.
Diving deeper into distress screening implementation in oncology care

Abstract Background Responding to calls for additional research that identifies effective distress screening (DS) processes, including referral practices subsequent to screening and receipt of recommended care, we engaged in qualitative research as part of a larger (mixed methods) study of distress screening. This qualitative inquiry of oncology professionals across different facilities in the United States examined routine DS implementation, facilitators and challenges staff encounter with DS processes, and staff members’ perceived value of DS. Participants and Methods We conducted key informant interviews and focus groups with staff in 4 Commission on Cancer (CoC)-accredited oncology facilities (a total of 18 participants) to understand implementation of routine DS within oncology care. We used a rigorous data analysis design, including inductive and deductive approaches. Results Respondents believe DS enhances patient care and described ways to improve DS processes, including administering DS at multiple points throughout oncology care, using patient-administrated DS methods, and enhancing electronic health records infrastructure to better collect, record, and retrieve DS data. Respondents also identified the need for additional psychosocial staff at their facilities to provide timely psychosocial care. Conclusions Results reinforce the value of DS in cancer care, including the importance of follow-up to screening with psychosocial oncology providers. Understanding and resolving the barriers and facilitators to implementing DS are important to ensure appropriate psychosocial care for people with cancer. Insights from oncology staff may be used to enhance the quality of DS and subsequent psychosocial care, which is an essential component of oncology care.
Curcumin and targeting of molecular and metabolic pathways in multiple sclerosis

Multiple sclerosis (MS) is a life‐threading disease that poses a great threat to the human being lifestyle. Having said extensive research in the realm of underlying mechanisms and treatment procedures, no definite remedy has been found. Over the past decades, many medicines have been disclosed to alleviate the symptoms and marking of MS. Meanwhile, the substantial efficacy of herbal medicines including curcumin must be underscored. Accumulated documents demonstrated the fundamental role of curcumin in the induction of the various signaling pathways. According to evidence, curcumin can play a role in mitochondrial dysfunction and apoptosis, autophagy, and mitophagy. Also, by targeting the signaling pathways AMPK, PGC‐1α/PPARγ, and PI3K/Akt/mTOR, curcumin interferes with the metabolism of MS. The anti‐inflammatory, antioxidant, and immune regulatory effects of this herbal compound are involved in its effectiveness against MS. Thus, the present review indicates the molecular and metabolic pathways associated with curcumin's various pharmacological actions on MS, as well as setting into context the many investigations that have noted curcumin‐mediated regulatory effects in MS.
Radiation pressure torque and computational attitude modelling of space debris

Human space activity in the past 50 years has led to a plethora of man-made space debris which pose an imminent threat to global space operations. The current models of space debris orbits are not sufficient for detailed orbit prediction or for accurate tracking. This uncertainty manifests itself in Conjunction Analysis (CA) with active spacecraft, which leads to excessive orbital manoeuvres which are both expensive and reduce the lifetime of satellites. Advances in orbit modelling will lead to better prediction of debris orbits and reduce the need for collision avoidance manoeuvres, as well as minimising the future pollution of the space environment through collisions. Most existing methods for analysing the orbits of space debris do not take into account the effects of tumbling, and the attitude-dependent nonconservative forces are generally neglected. This study models the torques and attitude motion of uncontrolled man-made objects in orbit about the Earth, which tumble due to a combination of natural influences of the near-Earth space environment and initial angular momentum acquired during debris formation. The modelling of space debris is a relatively new field and represents a huge new area of research. The two main branches of this thesis are (a) modelling the torques that induce spin for objects in orbit, and (b) modelling the effect of certain attitude-dependent non-conservative forces on spinning objects in orbit. The main torque modelled in this study is solar radiation pressure (SRP). Simulations of the radiation-induced torques are performed and the main mechanisms that lead to the tumbling of uncontrolled objects are analysed. A novel method of presenting attitude-dependent forces and torques on space objects, dubbed ”Torque Maps”, is presented. Radiation torques are caused by optical geometric asymmetry and can lead to oscillatory and secular changes in attitude. They are computed for one of the largest objects in orbit: Envisat, a defunct satellite with complex geometry. Further to these, simulations of objects spinning in orbit are used to calculate the effect of tumbling on orbital motion. The results show that the effects of nonconservative forces on tumbling objects lead to both periodic and secular variations in their orbital elements. This is contrary to previously popular assumption. Additionally, ideas for utilising modern developments in nanosatellite technology for validation of orbit prediction models are presented and calculations of the Lorentz force and its effect for uncontrolled objects are given.
Causal Effects of YKL‐40 on Ischemic Stroke and Its Subtypes: A 2‐Sample Mendelian Randomization Study

Background Chitinase‐3 like protein 1 (CHI3L1, YKL‐40) was reported to be implicated in the development of ischemic stroke, but whether the association between them was causal remained unclear. We conducted a 2‐sample Mendelian randomization study to explore the associations of genetically determined plasma YKL‐40 with ischemic stroke and its subtypes (large artery stroke, small vessel stroke, and cardioembolic stroke). Methods and Results Based on genome‐wide association study data of 3394 European‐descent individuals, we selected 13 single‐nucleotide polymorphisms associated with plasma YKL‐40 as genetic instruments. Summary data about ischemic stroke and its subtypes were obtained from the Multiancestry Genome‐wide Association Study of Stroke Consortium, involving 34 217 ischemic stroke cases and 406 111 controls of European ancestry. We used the inverse‐variance weighted method followed by a series of sensitivity analyses to assess the causal associations of plasma YKL‐40 with ischemic stroke and its subtypes. The primary analysis showed that genetically determined high YKL‐40 levels were associated with increased risks of large artery stroke (odds ratio [OR], 1.08 [95% CI, 1.04–1.12]; P=1.73×10−4) and small vessel stroke (OR, 1.05 [95% CI, 1.01–1.09]; P=7.96×10−3) but not with ischemic stroke or cardioembolic stroke. Sensitivity analyses further confirmed these associations, and Mendelian randomization‐Egger indicated no evidence of genetic pleiotropy. In addition, supplementary analysis based on the summary data from the Olink proximity extension assay cardiovascular I (Olink CVD‐I) panel showed that high YKL‐40 levels were positively associated with the risks of large artery stroke (OR, 1.15 [95% CI, 1.08–1.22]; P=4.16×10−6) but not with small vessel stroke. Conclusions Genetically determined high plasma YKL‐40 levels were causal associated with increased risks of large artery stroke.
The curious case of Prevotella copri

ABSTRACT Prevotella copri is an abundant member of the human gastrointestinal microbiome, whose relative abundance has curiously been associated with positive and negative impacts on diseases, such as Parkinson’s disease and rheumatoid arthritis. Yet, the verdict is still out on the definitive role of P. copri in human health, and on the effect of different diets on its relative abundance in the gut microbiome. The puzzling discrepancies among P. copri studies have only recently been attributed to the diversity of its strains, which substantially differ in their encoded metabolic patterns from the commonly used reference strain. However, such strain differences cannot be resolved by common 16S rRNA amplicon profiling methods. Here, we scrutinize P. copri, its versatile metabolic potential, and the hypotheses behind the conflicting observations on its association with diet and human health. We also provide suggestions for designing studies and bioinformatics pipelines to better research P. copri.
Extremely Low Electron-ion Temperature Relaxation Rates in Warm Dense Hydrogen: Interplay between Quantum Electrons and Coupled Ions.

Theoretical and computational modeling of nonequilibrium processes in warm dense matter represents a significant challenge. The electron-ion relaxation process in warm dense hydrogen is investigated here by nonequilibrium molecular dynamics using the constrained electron force field (CEFF) method. CEFF evolves wave packets that incorporate dynamic quantum diffraction that obviates the Coulomb catastrophe. Predictions from this model reveal temperature relaxation times as much as three times longer than prior molecular dynamics results based on quantum statistical potentials. Through analyses of energy distributions and mean free paths, this result can be traced to delocalization. Finally, an improved GMS [Gericke, Murillo, and Schlanges, Phys. Rev. E 78, 025401 (2008)PRESCM1539-375510.1103/PhysRevE.78. 025401] model is proposed, in which the Coulomb logarithms are in good agreement with CEFF results.