Miracle-dz/UniFAR-FTUs huggingface dataset:
Making Olympic lizards: the effects of specialised exercise training on performance

ABSTRACT Exercise training is well known to affect a suite of physiological and performance traits in mammals, but effects of training in other vertebrate tetrapod groups have been inconsistent. We examined performance and physiological differences among green anole lizards (Anolis carolinensis) that were trained for sprinting or endurance, using an increasingly rigorous training regimen over 8 weeks. Lizards trained for endurance had significantly higher post-training endurance capacity compared with the other treatment groups, but groups did not show post-training differences in sprint speed. Although acclimation to the laboratory environment and training explain some of our results, mechanistic explanations for these results correspond with the observed performance differences. After training, endurance-trained lizards had higher haematocrit and larger fast glycolytic muscle fibres. Despite no detectable change in maximal performance of sprint-trained lizards, we detected that they had significantly larger slow oxidative muscle fibre areas compared with the other treatments. Treatment groups did not differ in the proportion of number of fibre types, nor in the mass of most limb muscles or the heart. Our results offer some caveats for investigators conducting training research on non-model organisms and they reveal that muscle plasticity in response to training may be widespread phylogenetically. Summary: Specialised training in lizards leads to dramatic increases in performance and changes in physiology.
The Role of Metabolomics and Microbiology in Urinary Tract Infection

One of the common illnesses that affect women’s physical and mental health is urinary tract infection (UTI). The disappointing results of empirical anti-infective treatment and the lengthy time required for urine bacterial culture are two issues. Antibiotic misuse is common, especially in females who experience recurrent UTI (rUTI). This leads to a higher prevalence of antibiotic resistance in the microorganisms that cause the infection. Antibiotic therapy will face major challenges in the future, prompting clinicians to update their practices. New testing techniques are making the potential association between the urogenital microbiota and UTIs increasingly apparent. Monitoring changes in female urinary tract (UT) microbiota, as well as metabolites, may be useful in exploring newer preventive treatments for UTIs. This review focuses on advances in urogenital microbiology and organismal metabolites relevant to the identification and handling of UTIs in an attempt to provide novel methods for the identification and management of infections of the UT. Particular attention is paid to the microbiota and metabolites in the patient’s urine in relation to their role in supporting host health.
An Exploratory Bioinformatic Investigation of Cats’ Susceptibility to Coronavirus-Deriving Epitopes

Coronaviruses are highly transmissible and pathogenic viruses for humans and animals. The vast quantity of information collected about SARS-CoV-2 during the pandemic helped to unveil details of the mechanisms behind the infection, which are still largely elusive. Recent research demonstrated that different class I/II human leukocyte antigen (HLA) alleles might define an individual susceptibility to SARS-CoV-2 spreading, contributing to the differences in the distribution of the infection through different populations; additional studies suggested that the homolog of the HLA in cats, the feline leukocyte antigen (FLA), plays a pivotal role in the transmission of viruses. With these premises, this study aimed to exploit a bioinformatic approach for the prediction of the transmissibility potential of two distinct feline coronaviruses (FCoVs) in domestic cats (feline enteric coronavirus (FeCV) and feline infectious peritonitis virus (FIPV)) using SARS-CoV-2 as the reference model. We performed an epitope mapping of nonapeptides deriving from SARS-CoV-2, FeCV, and FIPV glycoproteins and predicted their affinities for different alleles included in the three main loci in class I FLAs (E, H, and K). The predicted complexes with the most promising affinities were then subjected to molecular docking and molecular dynamics simulations to provide insights into the stability and binding energies in the cleft. Results showed the FLA proteins encoded by alleles in the FLA-I H (H*00501 and H*00401) and E (E*01001 and E*00701) loci are largely responsive to several epitopes deriving from replicase and spike proteins of the analyzed coronaviruses. The analysis of the most affine epitope sequences resulting from the prediction can stimulate the development of anti-FCoV immunomodulatory strategies based on peptide drugs.
Direct separation of in vivo and in vitro am3 revertants in transgenic mice carrying the phix174 am3, cs70 vector

Target genes in most transgenic systems have higher spontaneous mutation frequencies than do endogenous mammalian genes. Spontaneous mutations in transgenes predominantly arise from three sources: (1) mutations fixed in the animals, (2) mutations arising from replication errors caused by damage to the DNA that may have occurred in vivo or in vitro and then was fixed during amplification of the vector in vitro, and (3) mutations arising during replication of non‐revertant phages in non‐permissive bacteria. An assay based on single bursts was developed to directly distinguish between the in vivo and in vitro origins of revertants. The size of the aliquot is determined by mutant frequency and is adjusted so that ideally no more than 10 to 20% of the aliquots contain a bacterial cell transformed with a mutant phage. Mutations are detected as revertants of an amber mutation (am3) in phiX174 am3, cs70. The minimum burst size of non‐revertant phiX am3, cs70 from splenic DNA on a permissive bacterial strain was larger than 30 plaque‐forming units (pfu). Based on this observation, a burst size of 31 plaque‐forming revertants was chosen as the minimum burst size of a fixed mutation. The single burst assay was tested on DNA from spleens of animals that were treated with 150 mg/kg 1‐ethyl‐1 nitrosurea. Only the fraction of aliquots with single bursts of revertants (> 30) increased in the treated animals compared to the controls. In contrast, there was no difference between treated and control animals for revertant frequencies calculated for burst sizes ≤30 pfu. Among the spontaneous mutations, only 30% were caused by mutations fixed in animals (i.e. burst size >30 pfu). Total average revertant frequency measured in DNA from treated animals was less than twofold more than the average spontaneous frequency (P = 0.048). When frequencies were based on burst sizes >30, there was a 4.6‐fold increase among treated animals compared with controls (P = 0.026). The single burst‐assay resulted in a more sensitive test for mutagenicity because it eliminated noise from in‐vitro mutations. Environ. Mol. Mutagen. 37:345–355, 2001 Published 2001 Wiley‐Liss, Inc.
History and importance of the Bosniak classification for complex renal cysts

Radiol Bras. 2014 Nov/Dez;47(6):IX The study of the urogenital system has been subject of interest amongst the Brazilian radiological community. In the context of this subspecialty, renal cystic lesions constitute an extremely frequent finding (in 50% of the population above the age of 50), sometimes representing a great challenge in daily radiological practice. This theme of high relevance is constantly object of debate among surgeons and medical imaging professionals, since the differentiation between benign complex cysts and renal cystic carcinomas is of paramount relevance for the choice of the therapeutic approach. Considering the importance and complexity of renal cysts presentation, Morton A. Bosniak, in 1986, published a study proposing a categorization of such lesions in order to standardize the description of such lesions and their approach based on findings at intravenous contrast-enhanced computed tomography. The original description proposed by Bosniak for 28 years ago is widely used nowadays with few changes, corroborating the relevance of a full command of the classification of these lesions by radiologists and urologists in their daily practices. Initially, the cysts were classified from I to IV, where I corresponded to a simple cyst; II, a minimally complex cyst with low malignancy probability; III, a complex cyst with moderate malignancy probability; and IV, a cyst with a frankly solid component and high malignancy probability. The categories I and IV have always presented a great interobserver agreement in relation to their descriptions and approach, but, at the first years, there was a great interobserver disagreement in relation to the categories II and III. As a cyst was not sufficiently complex to fulfill the characteristics to be included in category III, but presented with somewhat complex characteristics to be classified as II, questionings were raised as regards the approach to be adopted, i.e., surgical approach for category III and finishing investigation for category II. Then, the category IIF was created, suggesting serial imaging follow-up for cysts with those characteristics. Over almost 30 years of the Bosniak classification, several studies have been published with numbers which corroborate the efficacy and reproducibility of such classification in the radiologists’ daily practice. For this reason, the review article published by Muglia and Westphalen in the present issue of Radiologia Brasileira is extremely important as the authors make a historical review of the main publications approaching the theme, with an overview of the classification in the current days, focusing on
Effectiveness of Group Physical Exercise in Treating Major Depressive Disorder: An Analysis of Secondary Data from an Aborted Randomized Trial

Background: Depression is highly prevalent and a significant cause of mortality and morbidity across the globe. Although antidepressants and/or psychotherapy are often used to treat depression, some recent studies indicate that exercise may play an important role in lowering depression symptoms among patients meeting the clinical criteria of a depressive episode. Objectives: This study aimed to evaluate the mental health and wellbeing of adult participants diagnosed with major depressive disorder (MDD) after fourteen weeks of receiving a supervised physical exercise program. Methods: In a pre-post design, the assessments were performed at baseline, seven weeks and fourteen weeks following the exercise intervention program using facilitated self-reported psychometric scales. The Beck Depression Inventory (BDI-2) and Clinical Outcomes in Routine Evaluation—Outcome Measure (CORE-OM) were used to assess depression. The short form of the International Physical Activity Questionnaire (IPAQ) was used for the self-reporting of participants’ physical activity. Results: At the beginning of the study, the baseline total mean scores and standard deviations for the BDI-2, CORE-OM, and IPAQ in both genders did not differ significantly (p-value > 0.05). Patients showed significant improvement in all assessment scales after completing fourteen weeks of the physical exercise program. Based on the BDI-2, the baseline score dropped from 31.25 (indicating moderate to severe depression) to 14.25 (indicating mild to minimal depression), with a p-value of <0.001. The CORE-OM total mean score was reduced from 1.91 to 0.98 with a significant p-value < 0.005 indicating effective clinical improvement in depression symptoms. The IPAQ total MET-minutes/week mean score increased from 1713.22 to 4367.62, indicating an improvement in the participants’ weekly P.E. intake; however, the change was not statistically significant (p = 0.07). Conclusions: Exercise treatment is linked with considerable therapeutic improvement in patients with MDD, particularly when exercise is sustained over time. The BDI-2 and CORE-OM total scores significantly decreased after the fourteen-week P.E. programme, indicating a change from moderate and severe depression to minimal and mild depression. Our findings offer insightful information to primary care doctors and psychiatrists, indicating that prescribing exercise to depressed patients may be a helpful adjunctive therapy.
Epidemiological characteristics and low case fatality rate of pandemic (H1N1) 2009 in Japan

Pandemic (H1N1) 2009 has been causing large outbreaks in Japan. Yet, the case fatality rate (CFR) remains low and only 85 deaths have been confirmed as of December 17, 2009. Surveillance data was analyzed to define epidemiological characteristics of pandemic (H1N1) 2009 in Japan. It was shown that most of the reported influenza-like illness cases and hospitalizations have occurred in those aged 5–9 years and 10–14 years, in whom CFR is extremely low. However, CFRs are higher in small children (<5 years) and adults. The transmission to these age groups may possibly have been minimized through aggressive suspension of classes in schools.
Eurasian aspen (Populus tremula L.): Central Europe’s keystone species ‘hiding in plain sight’

Knowledge of Eurasian aspen’s (Populus tremula L.) ecological and growth characteristics is of high importance to plant and wildlife community ecology, and noncommercial forest ecosystem services. This research assessed these characteristics, identified aspen’s habitat optimum, and examined causality of its current scarce distribution in central Europe. We analyzed a robust database of field measurements (4,656,130 stands) for forest management planning over 78,000 km2 of the Czech territory. Our analysis we used GIS techniques, with basic and multivariate statistics such as general linear models, ordination, and classification. Results describe a species of broad ecological amplitude that has heretofore attracted little research attention. Spatial analysis showed significant differences between aspen and other forest non-forest cover types. Additionally, we found significant association between the proportion of aspen in a stand, the size of forest property, and the forest category. The results demonstrate historic reasons for aspen’s widespread presence, though contemporary occurrence is limited. This study advances the concept of a quantitatively based aspen ecological optimum (niche), which we believe may be beneficial for numerous aspen associates in the context of anticipated warming. Irrespective of local ecology (i.e., the realized aspen niche), the study confirms that profit-driven policy in forestry is chiefly responsible for historic aspen denudation in central Europe. Even so, we demonstrate that ample habitat is present. Further solutions for improving aspen resilience are provided to support these keystone systems so vital to myriad dependent flora and fauna.
Object views: fine-grained sharing in browsers

Browsers do not currently support the secure sharing of JavaScript objects between principals. We present this problem as the need for object views, which are consistent and controllable versions of objects. Multiple views can be made for the same object and customized for the recipients. We implement object views with a JavaScript library that wraps shared objects and interposes on all access attempts. The security challenge is to fully mediate access to objects shared through a view and prevent privilege escalation. We discuss how object views can be deployed in two settings: same-origin sharing with rewriting-based JavaScript isolation systems like Google Caja, and inter-origin sharing between browser frames over a message-passing channel. To facilitate simple document sharing, we build a policy system for declaratively defining policies for document object views. Notably, our document policy system makes it possible to hide elements without breaking document structure invariants. Developers can control the fine-grained behavior of object views with an aspect system that accepts programmatic policies.
Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population

In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10–20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions.
Effects of cleft lip on visual scanning and neural processing of infant faces

Infant faces readily capture adult attention and elicit enhanced neural processing, likely due to their importance evolutionarily in facilitating bonds with caregivers. Facial malformations have been shown to impact early infant-caregiver interactions negatively. However, it remains unclear how such facial malformations may impact early visual processing. The current study used a combination of eye tracking and electroencephalography (EEG) to investigate adults’ early visual processing of infant faces with cleft lip/palate as compared to normal infant faces, as well as the impact cleft palate has on perceived cuteness. The results demonstrated a significant decrease in early visual attention to the eye region for infants with cleft palate, while increased visual attention is registered on the mouth region. Increased neural processing of the cleft palate was evident at the N170 and LPP, suggesting differences in configural processing and affective responses to the faces. Infants with cleft palate were also rated significantly less cute than their healthy counterparts (mean difference = .73, p < .001). These results suggest that infants’ faces with cleft lip/palate are processed differently at early visual perception. These processing differences may contribute to several important aspects of development (e.g., joint attention) and may play a vital role in the previously observed difficulties in mother-infant interactions.
Effects of trunk stabilization exercises on balance, functionality and abdominal muscle thickness in hemiplegic patients

Objectives This study aims to investigate the effects of trunk stabilization exercises (TSEs) in addition to conventional exercises in patients with stroke on balance, functionality and abdominal muscle thickness as measured by ultrasonography (USG) and to compare the patients’ non-paretic side abdominal muscle thickness with healthy population. Patients and methods Between April 2019 and June 2019, a total of 26 hemiparesis/hemiplegic patients with stroke (15 males, 11 females; mean age: 62.3±7.8 years; range, 52 to 71 years) confirmed by neurological examination or computed tomography (CT) / magnetic resonance imaging (MRI) and 20 age-matched healthy volunteers (12 males, 8 females; mean age: 62.3±7.2 years; range, 53 to 70 years) were included in the study. The patients were randomized into two groups. In the first group (n=13), TSE were performed in addition to conventional neurorehabilitation program, five times/week for a total of four weeks. The second group (n=13) was given conventional neurorehabilitation program, five times/week for a total of four weeks. Also, healthy volunteers as the third group were compared with the patient population. The evaluations were made at the beginning and end of the treatment. The Berg Balance Scale (BBS), Barthel Index (BI), Postural Assessment Scale for Stroke Patients (PASS), and Functional Reach Test (FRT) were used. Abdominal muscle thickness at rest and contraction were evaluated using USG. Results Ten patients in Group 1 and 10 patients in Group 2 completed study. A significant improvement was observed in all abdominal muscles in both groups (p<0.05), indicating no significant difference between the groups (p>0.05). There was a statistically significant improvement for BBS and FRT in both groups. The PASS and BI scores showed a significant improvement only in TSE group. Conclusion Both the TSE and conventional neurorehabilitation program provided significant improvements in abdominal muscle thickness, balance and trunk control. For postural control and functionality, additional TSE seems to be more effective.
Using Query Patterns to Learn the Duration of Events

We present the first approach to learning the durations of events without annotated training data, employing web query patterns to infer duration distributions. For example, we learn that "war" lasts years or decades, while "look" lasts seconds or minutes. Learning aspectual information is an important goal for computational semantics and duration information may help enable rich document understanding. We first describe and improve a supervised baseline that relies on event duration annotations. We then show how web queries for linguistic patterns can help learn the duration of events without labeled data, producing fine-grained duration judgments that surpass the supervised system. We evaluate on the TimeBank duration corpus, and also investigate how an event's participants (arguments) effect its duration using a corpus collected through Amazon's Mechanical Turk. We make available a new database of events and their duration distributions for use in research involving the temporal and aspectual properties of events.
Inferring HIV Escape Rates from Multi-Locus Genotype Data

Cytotoxic T-lymphocytes (CTLs) recognize viral protein fragments displayed by major histocompatibility complex molecules on the surface of virally infected cells and generate an anti-viral response that can kill the infected cells. Virus variants whose protein fragments are not efficiently presented on infected cells or whose fragments are presented but not recognized by CTLs therefore have a competitive advantage and spread rapidly through the population. We present a method that allows a more robust estimation of these escape rates from serially sampled sequence data. The proposed method accounts for competition between multiple escapes by explicitly modeling the accumulation of escape mutations and the stochastic effects of rare multiple mutants. Applying our method to serially sampled HIV sequence data, we estimate rates of HIV escape that are substantially larger than those previously reported. The method can be extended to complex escapes that require compensatory mutations. We expect our method to be applicable in other contexts such as cancer evolution where time series data is also available.