Miracle-dz/UniFAR-FTUs huggingface dataset:
Modularity‐based parallel protein design algorithm with an implementation using shared memory programming

Given a target protein structure, the prime objective of protein design is to find amino acid sequences that will fold/acquire to the given three‐dimensional structure. The protein design problem belongs to the non‐deterministic polynomial‐time‐hard class as sequence search space increases exponentially with protein length. To ensure better search space exploration and faster convergence, we propose a protein modularity–based parallel protein design algorithm. The modular architecture of the protein structure is exploited by considering an intermediate structural organization between secondary structure and domain defined as protein unit (PU). Here, we have incorporated a divide‐and‐conquer approach where a protein is split into PUs and each PU region is explored in a parallel fashion. It has been further analyzed that our shared memory implementation of modularity‐based parallel sequence search leads to better search space exploration compared to the case of traditional full protein design. Sequence‐based analysis on design sequences depicts an average of 39.7% sequence similarity on the benchmark data set. Structure‐based comparison of the modeled structures of the design protein with the target structure exhibited an average root‐mean‐square deviation of 1.17 Å and an average template modeling score of 0.89. The selected modeled structures of the design protein sequences are validated using 100 ns molecular dynamics simulations where 80% of the proteins have shown better or similar stability to the respective target proteins. Our study informs that our modularity‐based protein design algorithm can be extended to protein interaction design as well.
Muscle repair after physiological damage relies on nuclear migration for cellular reconstruction

Description Muscle repair without stem cells Skeletal muscle is a mechanical organ that endures cellular damage after contraction. Lesions caused by external injury can be repaired by muscle stem cells, which fuse with injured cells or create entirely new myofibers. Roman et al. describe a cell-autonomous repair process that is independent of muscle stem cells (see the Perspective by McNally and Demonbreun). After localized damage, myonuclei migrate to injury sites and locally deliver messenger RNA for cellular reconstruction. This myofiber self-repair represents a model for understanding the restoration of muscle architecture in health and disease. —BAP Muscle cell nuclei migrate to myofiber lesions to deliver mRNA locally for cellular repair. Regeneration of skeletal muscle is a highly synchronized process that requires muscle stem cells (satellite cells). We found that localized injuries, as experienced through exercise, activate a myofiber self-repair mechanism that is independent of satellite cells in mice and humans. Mouse muscle injury triggers a signaling cascade involving calcium, Cdc42, and phosphokinase C that attracts myonuclei to the damaged site via microtubules and dynein. These nuclear movements accelerate sarcomere repair and locally deliver messenger RNA (mRNA) for cellular reconstruction. Myofiber self-repair is a cell-autonomous protective mechanism and represents an alternative model for understanding the restoration of muscle architecture in health and disease.
Efficacy, tolerability, and safety of montelukast versus finasteride for the treatment of moderate acne in women: A prospective, randomized, single‐blinded, active‐controlled trial

Acne is a chronic inflammatory skin disease which involves the pilosebaceous unit. Tissue inflammation isone of the crucial mechanisms, amongst others. Of the various cytokines, leukotriene B4 (LT‐B4) is the most potentleucocyte chemotactic mediator. Montelukast is an antagonist of the LT‐B4 receptor. Finasteride is an antiandrogen whichspecifically inhibits the 5α‐reductase enzyme.
Remdesivir Efficacy in COVID-19 Treatment: A Randomized Controlled Trial

ABSTRACT. To date, no antiviral therapy has shown proven clinical effectiveness in treating patients with COVID-19. We assessed the efficacy of remdesivir in hospitalized Egyptian patients with COVID-19. Patients were randomly assigned at a 1:1 ratio to receive either remdesivir (200 mg on the first day followed by 100 mg daily for the next 9 days intravenously infused over 30–60 minutes) in addition to standard care or standard care alone. The primary outcomes were the length of hospital stay and mortality rate. The need for mechanical ventilation was assessed as a secondary outcome. Two hundred patients (100 in each group) completed the study and were included in the final analysis. The remdesivir group showed a significantly lower median duration of hospital stay (10 days) than the control group (16 days; P < 0.001). Eleven of the patients in the remdesivir group needed mechanical ventilation compared with eight patients in the control group (P = 0.469). The mortality rate was comparable between the two groups (P = 0.602). Mortality was significantly associated with older age, elevated C-reactive protein levels, elevated D-dimer, and the need for mechanical ventilation (P = 0.039, 0.003, 0.001, and < 0.001 respectively). Remdesivir had a positive influence on length of hospital stay, but it had no mortality benefit in Egyptian patients with COVID-19. Its use, in addition to standard care including dexamethasone, should be considered, particularly in low- and middle-income countries when other effective options are scarce.
The effects of specialized emergency and intensive nursing team on arterial blood gas and pulmonary function in pulmonary infection with respiratory failure.

OBJECTIVE To investigate effects of specialized emergency and intensive nursing team on arterial blood gas and pulmonary function in pulmonary infected patients with respiratory failure. METHODS 126 patients with pulmonary infection and respiratory failure admitted to our hospital were chosen and randomly divided into observation group and control group, with 63 cases in each group. The control-group received specialized routine nursing care, and the observation-group was treated with the emergency and intensive nursing care. Subsequently, the arterial blood gas, pulmonary function, inflammatory biomarkers, complication rate, recovery course and nursing satisfaction between the two groups were compared accordingly. RESULTS After nursing care, the arterial blood gas and pulmonary function indexes of the two groups were remarkably improved than before, and the improvement in observation-group was superior to that in control-group (P<0.05); The inflammatory indicators of hs-CRP and PCT in two groups decreased substantially than before, and observation-group had remarkably lower indicators than that of the control-group (P<0.05); The incidence of complications in observation-group was 4.76%, significantly lower than 19.05% in control-group (P<0.05); The objects in observation-group spent exactly shorter time on ventilator than whom in control-group, and the difference was statistically significant (P<0.05); The observation-group had critically shorter length of hospital stay than those in control-group (P<0.05). The satisfaction of the observation-group with nursing care was 93.65%, which was dramatically higher than 73.02% in control-group (P<0.05). CONCLUSIONS For pulmonary infection and respiratory failure, the nursing intervention carried by the specialized emergency and intensive nursing team can remarkably improve the arterial blood gas and pulmonary function, reduce the patients' inflammatory indicators and incidence of complications. The application of the nursing team can reduce the time on ventilator and length of hospital stay, and improve patients' satisfaction with nursing care.
Assessment of Sacsin Turnover in Patients With ARSACS

Background and Objectives Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is caused by variations in SACS gene encoding sacsin, a huge multimodular protein of unknown function. More than 200 SACS variations have been described worldwide to date. Because ARSACS presents phenotypic variability, previous empirical studies attempted to correlate the nature and position of SACS variations with the age at onset or with disease severity, although not considering the effect of the various variations on protein stability. In this work, we studied genotype-phenotype correlation in ARSACS at a functional level. Methods We analyzed a large set of skin fibroblasts derived from patients with ARSACS, including both new and already published cases, carrying variations of different types affecting diverse domains of the protein. Results We found that sacsin is almost absent in patients with ARSACS, regardless of the nature of the variation. As expected, we did not detect sacsin in patients with truncating variations. We found it strikingly reduced or absent also in compound heterozygotes carrying diverse missense variations. In this case, we excluded SACS mRNA decay, defective translation, or faster posttranslational degradation as possible causes of protein reduction. Conversely, our results demonstrate that nascent mutant sacsin protein undergoes cotranslational ubiquitination and degradation. Discussion Our results provide a mechanistic explanation for the lack of genotype-phenotype correlation in ARSACS. We also propose a new and unambiguous criterion for ARSACS diagnosis that is based on the evaluation of sacsin level. Last, we identified preemptive degradation of a mutant protein as a novel cause of a human disease.
Reliability of radiographic findings in large FOV CBCTs of mandibular third molars as basis for pre-operative patient information

Abstract Objective The aim of this study was to assess the relation between radiographic findings in large field of view (FOV) cone beam computed tomography (CBCT) exams and clinical findings of mandibular third molars in relation to the pre-operative patient information. Material and Methods Two hundred and nine mandibular third molars in 134 orthognathic patients examined with CBCT were removed. Three observers assessed tooth- and mandibular canal-related variables in CBCT images, and the findings were correlated to clinical findings during surgery for all observers: tooth angulation, number and morphology of roots and close relationship between the tooth and the mandibular canal. Moreover, positive (PPV) and negative (NPV) predictive values and positive (LR+) and negative (LR-) likelihood ratios were calculated for the canal-related variables. Inter- and intra-observer reproducibility was expressed as percentage accordance and kappa-statistics. Results Generally, there was high correlation between radiographic and clinical tooth-related variables. The opposite was true for the canal-related variables, since the PPV and LR + were low. The highest PPV and LR + were found when the mandibular canal was positioned between the roots of the third molar. Conclusions Tooth-related findings in CBCT are reliable, whereas mandibular canal-related findings should not affect the information provided to the patient pre-operatively.
Co-application of thifensulfuron with glyphosate accentuates soybean injury

Abstract: Three trials (two in 2019 and one in 2020) were completed at the University of Guelph, Huron Research Station near Exeter, ON, to determine if the co-application of thifensulfuron with glyphosate accentuates soybean injury in glyphosate-resistant (GR) soybean. At 1, 2, 4, and 8 weeks after treatment (WAT), thifensulfuron (6 and 12 g a.i.·ha−1 representing the 1× and 2× rate, respectively) applied POST with no adjuvants caused up to 5% soybean injury. The addition of a non-ionic surfactant + UAN to thifensulfuron increased soybean injury to up to 24%. There was no decrease in soybean density, dry biomass, height, and yield, except soybean dry biomass was reduced up to 22% with the addition of adjuvants to thifensulfuron at the 2× rate. Glyphosate (1800 and 3600 g·ha−1 representing the 1× and 2× rate, respectively) applied POST caused no adverse effect on soybean injury parameters evaluated. The co-application of glyphosate + thifensulfuron at the 1× and 2× rates, without additional adjuvants, caused a synergistic increase in soybean injury at 1, 2, 4, and 8 WAT, and a synergistic decrease in dry biomass and height. All other interactions were additive. The co-application of glyphosate + thifensulfuron at the 1× and 2× rates, with additional adjuvants, produced a synergistic increase in injury at 1 (1× and 2× rate), 4 (1× rate), and 8 (1× rate) WAT in soybean. All other interactions were additive.
A Theory-Practice Divide in a Museum Showcase

Abstract We aim to map the divide between practice and research in the field of knowledge production and diffusion related to museum studies. In doing so, we draw on the domain literature regarding the evolution of museums as institutions and its implications for the development of a dedicated field of studies. The current research focuses on the publishing work undertaken by museum professionals and researchers, as an essential component contributing to the advancement of research as well as to the diffusion of good practices. More precisely, we scrutinized European journals from the domain available on the Web of Science (WoS) as well as journals not included in the “main” scientific flows and generally published in various languages, other than English.
The effects of vitamin D, fish oil and exercise on cardiovascular parameters in ovariectomized rats

Abstract Objectives This study compared effects of vitamin D, fish oil and exercise on cardiovascular parameters in ovariectomized rats. Materials and methods This is an experimental study conducted with 45 female Wistar Albino rats; consisted of one sham (n=8) and four intervention (n=37) groups. Rats (n=37) were oophorectomized and, randomly divided into four groups at the end of the first week following wound healing. Interventions were applied to the groups of oophorectomize+Dvit, oophorectomize+fish oil and oophorectomize+exercise for 12 weeks. In analyzing the data, ANOVA and Tamhane’s T2 tests were used (p<0.05). Results The levels of total-cholesterol (66.7 ± 7.6 mg/dL), HDL-cholesterol (33.8 ± 2.1 mg/dL), TOS (7.3 ± 1.2 μmol H2O2 Eq/L), TAS (4.0 ± 0.5 mmol Trolox Eq/L), OSI (0.2 ± 0.1) and total-cholesterol/HDL-cholesterol (2.0 ± 0.3) were obtained significant in exercising oophorectomized rats according to the oophorectomized rats (p<0.05). The estrogen levels of rats using vitamin D and fish oil and exercising were found to be higher than those in menopause. Conclusions It was concluded that exercising oophorectomized rats had a lower risk of cardiovascular disease. In this context, exercise/physical activity should be recommended and must be supported for practicing in order to protect the cardiovascular health of postmenopausal women.
Innovative Behavior and Firm Competitive Advantage: The Moderating Effect of Environmental Dynamism

Abstract The study investigated the effect of innovative behavior of managers on the competitive advantage of small, medium, and micro enterprises (SMMEs) in South Africa. In addition, the study examined the moderating role of environmental dynamism in the relationship between innovative behavior and competitive advantage. The study adopted the quantitative research design, and the cross-sectional survey method was used for data collection. Hierarchical regression was used for data analysis. Based on a dataset of 140 respondents, the results indicated that innovative behavior has a significant positive impact on competitive advantage. The moderating effect of environmental dynamism is insignificant. Theoretically, the study explains the moderating effect of environmental dynamism in the relationship between innovative behavior and firm competitive advantage. To sustain competitive advantage, it is important for firms to invest in the innovative behavior of managers and employees through training. Management must foster an environment that support the generation of new ideas by employees and the coordination of such ideas to improve products and services.
Early Neolithic Husbandry in the Pre-Pyrenean Area. The Management of Herds at the Cova Colomera (Serra del Montsec, Spain) and Its Implications for the Early Occupation of the Region

Abstract The Cova Colomera is located in the pre-Pyrenees, at a central point of a set of natural paths traditionally used by shepherds for herd movements. The Early Neolithic occupations documented in this cave (5250–4780 cal. BC) make it a key point for understanding the beginning of husbandry in the area. In this work, we present a zooarchaeological study of the macrofaunal remains recovered from these Early Neolithic occupations of the Cova Colomera. As observed at other sites in the region, the herds that occupied the Cova Colomera were mainly composed of domestic sheep and goats, raised for their milk and meat. Cattle, as well as a variety of wild animals, served as a food supplement and a source of secondary resources. The low number of recovered remains is interpreted as evidence of the low intensity and/or short duration of the occupations, which would have taken place at different times of the year, mainly in spring and autumn. This suggests that the Cova Colomera was used as a transient settlement during the movement of flocks. The data corroborate the idea that the natural resources of the pre-Pyrenees were exploited by the earliest shepherds in the Early Neolithic.
Evaluation of COVID-19 vaccine breakthrough infections among immunocompromised patients fully vaccinated with BNT162b2

Abstract Objective To evaluate COVID-19 vaccine breakthrough infections among immunocompromised (IC) individuals. Methods Individuals vaccinated with BNT162b2 were selected from the US HealthVerity database (10 December 2020 to 8 July 2021). COVID-19 vaccine breakthrough infections were examined in fully vaccinated (≥14 days after 2nd dose) IC individuals (IC cohort), 12 mutually exclusive IC condition groups, and a non-IC cohort. IC conditions were identified using an algorithm based on diagnosis codes and immunosuppressive (IS) medication usage. Results Of 1,277,747 individuals ≥16 years of age who received 2 BNT162b2 doses, 225,796 (17.7%) were identified as IC (median age: 58 years; 56.3% female). The most prevalent IC conditions were solid malignancy (32.0%), kidney disease (19.5%), and rheumatologic/inflammatory conditions (16.7%). Among the fully vaccinated IC and non-IC cohorts, a total of 978 breakthrough infections were observed during the study period; 124 (12.7%) resulted in hospitalization and 2 (0.2%) were inpatient deaths. IC individuals accounted for 38.2% (N = 374) of all breakthrough infections, 59.7% (N = 74) of all hospitalizations, and 100% (N = 2) of inpatient deaths. The proportion with breakthrough infections was 3 times higher in the IC cohort compared to the non-IC cohort (N = 374 [0.18%] vs. N = 604 [0.06%]; unadjusted incidence rates were 0.89 and 0.34 per 100 person-years, respectively. Organ transplant recipients had the highest incidence rate; those with >1 IC condition, antimetabolite usage, primary immunodeficiencies, and hematologic malignancies also had higher incidence rates compared to the overall IC cohort. Incidence rates in older (≥65 years old) IC individuals were generally higher versus younger IC individuals (<65). Limitations This retrospective analysis relied on coding accuracy and had limited capture of COVID-19 vaccine receipt. Conclusions COVID-19 vaccine breakthrough infections are rare but are more common and severe in IC individuals. The findings from this large study support the FDA authorization and CDC recommendations to offer a 3rd vaccine dose to increase protection among IC individuals.
Differential Association of Free, Conjugated, and Bound Forms of Polyamines and Transcript Abundance of Their Biosynthetic and Catabolic Genes During Drought/Salinity Stress in Tomato (Solanum lycopersicum L.) Leaves

Polyamines have been implicated in ameliorating the detrimental effects of drought and saline conditions on plant growth and development. The independent impact of these two abiotic stresses on polyamine (PA) biosynthesis, catabolism, and homeostasis, as well as on their transcript abundance in tomato leaves, is presented here. We show that the total levels of putrescine (PUT), spermidine (SPD), and spermine (SPM) increase up to 72 h during drought and up to 48 h during salinity stress before their precipitable drop thereafter. Thus, tomato plants maintain survivability to drought as well as salinity stress for up to 3 and 2 days, respectively. Independent multivariant analyses of drought and salinity stress kinetic data separately showed a closer association with levels of free, conjugated, and bound forms of SPD and SPM, but not with free or bound PUT. However, combined multivariant analyses showed a closer association of free SPD, conjugated SPD, and bound SPD with both stresses; SPD-bound and SPM conjugated with drought; and free SPM and conjugated PUT with salinity stress, respectively. PA biosynthesis genes, ARG1, SPDS1, and SAMDc3, segregated with drought and SPDS2 with salinity stress. PA catabolic genes CuAO4-like and PAO4 were associated with drought and salinity stresses, respectively, suggesting differential involvement of PA biosynthesis and catabolic genes in drought and salinity stresses. Pearson correlation indicated mostly positive correlations between the levels of free, conjugated, and bound forms of PUT, SPD, and SPM under drought and salinity stress. However, negative correlations were mostly seen between the levels of various forms of the PAs and their biosynthesis/catabolic genes. Levels of different PA forms had a twofold higher negative correlation during drought as compared to salinity stress (66 vs. 32) and with transcript levels of PA biosynthesis and catabolic genes. Transcripts of light-harvesting chlorophyll a/b-binding genes were generally positively associated with different forms of PAs but negatively to carbon flow genes. Most of the PA biosynthesis genes were coordinately regulated under both stresses. Collectively, these results indicate that PAs are distinctly regulated under drought and salinity stress with different but specific homologs of PA biosynthesis and catabolic genes contributing to the accumulation of free, conjugated, and bound forms of PAs.
Functional Connectivity Analysis in Motor-Imagery Brain Computer Interfaces

Motor Imagery BCI systems have a high rate of users that are not capable of modulating their brain activity accurately enough to communicate with the system. Several studies have identified psychological, cognitive, and neurophysiological measures that might explain this MI-BCI inefficiency. Traditional research had focused on mu suppression in the sensorimotor area in order to classify imagery, but this does not reflect the true dynamics that underlie motor imagery. Functional connectivity reflects the interaction between brain regions during the MI task and resting-state network and is a promising tool in improving MI-BCI classification. In this study, 54 novice MI-BCI users were split into two groups based on their accuracy and their functional connectivity was compared in three network scales (Global, Large and Local scale) during the resting-state, left vs. right-hand motor imagery task, and the transition between the two phases. Our comparison of High and Low BCI performers showed that in the alpha band, functional connectivity in the right hemisphere was increased in High compared to Low aptitude MI-BCI users during motor imagery. These findings contribute to the existing literature that indeed connectivity might be a valuable feature in MI-BCI classification and in solving the MI-BCI inefficiency problem.