Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular systematics of Mus crociduroides, an endemic mouse of Sumatra (Muridae : Rodentia)

Des sequences completes du gene mitochondrial codant pour l'ARN 12S ont ete obtenues chez 11 especes de rongeurs Muridae afin d'etudier les relations evolutives de la souris Mus crociduroides, une espece endemique de l'ile de Sumatra. Des analyses phylogenetiques utilisant tant les distances que la parcimonie, et sur differents types de changements nucleotidiques (transitions, transversions, insertions et deletions), indiquent toutes que Mus crociduroides se groupe avec M. pahari, ces deux especes appartenant au sousgenre Coelomys. L'ordre de branchement entre les quatre sous-genres de souris (Mus sensu stricto, Pyromys, Coelomys, Nannomys) n'a pas pu etre determine, probablement a cause d'un echantillonnage trop restreint de genes et/ou de taxons representatifs. Tous les resultats moleculaires soutiennent la monophylie des souris du genre Mus sensu lato par rapport aux Murinae africains tels Mastomys erythroleucus ou Hylomyscus stella . Le mode d'evolution moleculaire du gene 12S, tel qu'observe chez les rongeurs Muridae, apparait original en ce sens que le rapport transitions : transversions est voisin de un, contrairement a ce qui est observe chez les autres mammiferes separes par des taux de divergence genetique similaires, ou les transitions sont beaucoup plus nombreuses que les transversions.
Reproducibility of the DrGoniometer app for field-based assessment of the break-point angle in Nordic Hamstring exercise

Smartphone-based measurement could represent a portable and cheap solution to assess the Nordic Hamstring break-point angle (BPA). We investigated the following: (1) the reproducibility of the DrGoniometer app, (2) its agreement with a computerized video analysis software used as a reference method, and (3) the effects of raters’ experience. Fifty recordings were processed by four independent raters. Intraclass correlation coefficient (ICC), SEM, and minimum detectable change (MDC) were calculated. Bland–Altman plots verified the limits of agreement (LoA) with the reference method. The effect of raters’ clinical experience was investigated by unpaired t-tests. The app showed excellent intra-rater (ICC = 0.89, 95% CI, 0.84–0.92) and inter-rater reliability (ICC = 0.82, 95% CI, 0.74–0.89), low error (SEM = 2°; MDC = 5.5°), and substantial agreement with video analysis [95% LoA = ±6.7°; mean difference = 1.0°]. Rater experience did not affect results (P > 0.05). The smartphone-based app offers a reliable, valid, quick, and portable method for measuring the BPA in Nordic Hamstring exercise.
Revised Self-Monitoring Scale

Objective To investigate whether the Revised Self-Monitoring Scale (RSMS), an informant measure of socioemotional sensitivity, is a potential clinical endpoint for treatment trials for patients with behavioral variant frontotemporal dementia (bvFTD). Methods We investigated whether RSMS informant ratings reflected disease severity in 475 participants (71 bvFTD mutation+, 154 bvFTD mutation−, 12 behavioral mild cognitive impairment [MCI] mutation+, 98 asymptomatic mutation+, 140 asymptomatic mutation−). In a subset of 62 patients (20 bvFTD mutation+, 35 bvFTD mutation−, 7 MCI mutation+) who had at least 2 time points of T1-weighted images available on the same 3T scanner, we examined longitudinal changes in RSMS score over time and its correspondence to progressive gray matter atrophy. Results RSMS score showed a similar pattern in mutation carriers and noncarriers, with significant drops at each stage of progression from asymptomatic to very mild, mild, moderate, and severe disease (F4,48 = 140.10, p < 0.001) and a significant slope of decline over time in patients with bvFTD (p = 0.004, 95% confidence interval [CI] −1.90 to −0.23). More rapid declines on the RSMS corresponded to faster gray matter atrophy predominantly in the salience network (SN), and RSMS score progression best predicted thalamic volume in very mild and mild disease stages of bvFTD. Higher RSMS score predicted more caregiver burden (p < 0.001, 95% CI −0.30 to −0.11). Conclusions The RSMS is sensitive to progression of both socioemotional symptoms and SN atrophy in patients with bvFTD and corresponds directly to caregiver burden. The RSMS may be useful in both neurologic practice and clinical trials aiming to treat behavioral symptoms of patients with bvFTD.
Correlation of Quantitative Myasthenia Gravis and Myasthenia Gravis Activities of Daily Living scales in the MGTX study

Quantitative Myasthenia Gravis (QMG) and Myasthenia Gravis Activities of Daily Living (MG‐ADL) scales were compared using the data from the Thymectomy Trial in Non‐Thymomatous Myasthenia Gravis Patients Receiving Prednisone Therapy (MGTX) study.
Heritability estimates for height for young interior spruce in British Columbia

Height growth for interior spruce (Piceaglauca (Moench) Voss and P. engelmannii Parry) after 3, 6, and 10 growing seasons was assessed in a progeny test of 174 wind-pollinated families at three test sites in north central British Columbia. Test sites had a major influence on the juvenile growth of interior spruce, reflecting differences in potential site productivity as well as the importance of good site preparation and subsequent brush control for spruce seedlings. Mean heights within and across sites differed among families. The 3- and 6-year family performances correlated with family performances at age 10. Family–site interaction was significant at the 1% probability level, but accounted for no more than a quarter of the family variance at the three assessment years. Performance of the top and bottom 25% of families was consistent across the three sites. The narrow-sense heritability estimates after the third, sixth, and tenth growing seasons were 0.52, 0.36, and 0.29, respectively. The corresponding.
Bone Marrow Aspirate Concentrate: Its Uses in Osteoarthritis

Human bone marrow (BM) is a kind of source of mesenchymal stem cells (MSCs) as well as growth factors and cytokines that may aid anti-inflammation and regeneration for various tissues, including cartilage and bone. However, since MSCs in BM usually occupy only a small fraction (0.001%) of nucleated cells, bone marrow aspirate concentrate (BMAC) for cartilage pathologies, such as cartilage degeneration, defect, and osteoarthritis, have gained considerable recognition in the last few years due to its potential benefits including disease modifying and regenerative capacity. Although further research with well-designed, randomized, controlled clinical trials is needed to elucidate the exact mechanism of BMAC, this may have the most noteworthy effect in patients with osteoarthritis. The purpose of this article is to review the general characteristics of BMAC, including its constituent, action mechanisms, and related issues. Moreover, this article aims to summarize the clinical outcomes of BMAC reported to date.
Ethyl Formate as a Methyl Bromide Alternative for Phytosanitary Disinfestation of Imported Banana in Korea With Logistical Considerations

Abstract Methyl bromide (MB) use for quarantine and phytosanitary purposes is being phased out. Several effective MB alternatives have been identified depending on the target system. Industry commitment for the shift to new technologies will depend not only on the efficacy of alternatives but also on their compatibility and integrability into existing operations. We compared the efficacy of MB and ethyl formate (EF) for disinfestation of Planococcus citri (Risso) (Hemiptera: Pseudococcidae) as a representative surface pest on banana and evaluated whether EF fumigation is compatible with the current packaging materials and loading ratio used by the South Korean banana import industry. Fumigation trials with P. citri adults and eggs showed that EF was at least as effective as MB at the EF and MB concentrations recommended under the current phytosanitary disinfestation guidelines. From a logistical standpoint, EF gas could not effectively penetrate plastic bagging typically used in banana cartons during commercial shipping. Also, EF sorption to bananas and packing materials (used as cushioning inside bagging) further lowered realized EF concentrations around bananas. These reductions in EF concentration translated into reduced mortality of P. citri eggs, indicating that despite similar efficacy of MB and EF for controlling P. citri, further consideration and optimization of other industry logistics such as packaging and loading ratio is necessary to enhance the adoption of this MB alternative.
Implications for the Multi-Disciplinary Management of Children With Craniofrontonasal Syndrome.

The purpose of this retrospective study was to assess the genetic and phenotypic features of patients with craniofrontonasal syndrome (CFNS), and the implications of the condition for multidisciplinary management.The subjects were 25 female patients with a mutation of EFNB1, who presented to the Oxford Craniofacial Unit during a 38-year period. Medical records were reviewed for genetic and phenotypic information. Mean duration of follow-up was 12.6 years (range 0-30.7 years). This study examines neurodevelopment in constituent parts, with specific reference to speech, language, and cognition in relation to genotype. Three children had deletions extending beyond the EFNB1 gene; the 2 with available data presented with speech, language, or cognitive delay. The remaining 25 patients had intragenic mutations of EFNB1. Of these 25, those assessed in detail showed variable difficulties with speech and language development; 57% had receptive language difficulties (n = 4/7) and 88% had expressive language difficulties (n = 8/9). 55% presented with speech difficulties (n = 6/11). 2/3 patients with abnormal hearing had speech difficulties; 4/5 with normal hearing had normal speech development. Cognitive assessments indicated that IQ is variable; with full scale IQ ranging from 69 to 100.The complex, multifactorial presentation of patients with CFNS contributed to 41% (n = 7/17) of patients requiring additional educational support.Our results demonstrated significant multidisciplinary input is required, including Speech and Language Therapy, Plastic and Reconstructive Surgery, Genetics, Ear, Nose and Throat, Maxillofacial, Orthodontic, Orthopaedic, Clinical Psychology and Orthoptic teams. The results of this study reinforce the importance of multi-disciplinary long-term follow-up of children with CFNS.
The Roles of Disliking, Deservingness, and Envy in Predicting Schadenfreude

Schadenfreude (pleasure about another’s misfortune) was studied using written scenarios that were manipulated to include elements that elicited disliking of the target, envy of the target, and/or deservingness of the misfortune. This was the first time all the three predictors were included in a single study, allowing for a test of their possible interactive effects. Study 1 created a large pool of scenarios based on a pilot study and had participants rate them regarding how much disliking, deservingness, or envy was felt. The eight scenarios that were most effective in eliciting the various combinations of predictors were then used in Study 2 to test for schadenfreude reactions. Results revealed strong main effects for disliking and deservingness. Interactions showed that disliking attenuated the effect of deservingness, especially for female participants. Finally, further evidence was found that malicious but not benign envy predicted schadenfreude.
Improving Prediction Accuracy Using Multi-allelic Haplotype Prediction and Training Population Optimization in Wheat

The use of haplotypes may improve the accuracy of genomic prediction over single SNPs because haplotypes can better capture linkage disequilibrium and genomic similarity in different lines and may capture local high-order allelic interactions. Additionally, prediction accuracy could be improved by portraying population structure in the calibration set. A set of 383 advanced lines and cultivars that represent the diversity of the University of Minnesota wheat breeding program was phenotyped for yield, test weight, and protein content and genotyped using the Illumina 90K SNP Assay. Population structure was confirmed using single SNPs. Haplotype blocks of 5, 10, 15, and 20 adjacent markers were constructed for all chromosomes. A multi-allelic haplotype prediction algorithm was implemented and compared with single SNPs using both k-fold cross validation and stratified sampling optimization. After confirming population structure, the stratified sampling improved the predictive ability compared with k-fold cross validation for yield and protein content, but reduced the predictive ability for test weight. In all cases, haplotype predictions outperformed single SNPs. Haplotypes of 15 adjacent markers showed the best improvement in accuracy for all traits; however, this was more pronounced in yield and protein content. The combined use of haplotypes of 15 adjacent markers and training population optimization significantly improved the predictive ability for yield and protein content by 14.3 (four percentage points) and 16.8% (seven percentage points), respectively, compared with using single SNPs and k-fold cross validation. These results emphasize the effectiveness of using haplotypes in genomic selection to increase genetic gain in self-fertilized crops.
Rheology of Water Flows Confined Between Multi-Layer Graphene Walls.

Water confined by hydrophilic materials shows unique transport properties compared to bulk water thereby offering new opportunities for development of nano-fluidic devices. Recent experimental and numerical studies showed that nano-confined water undergoes liquid-to-solid phase-like transitions depending on the degree of confinement. In the case of water confined by graphene layers, the Van der Waals forces are known to deform the graphene layers, whose bending leads to further non-uniform confinement effects. Despite the extensive studies of nano-confined water at equilibrium conditions, the interplay between the confinement and rheological water properties, such as viscosity, slip length and normal stress differences under shear flow conditions, is poorly understood. The current investigation uses a validated all-atom non-equilibrium molecular dynamics model to simultaneously analyse continuum transport and atomistic structure properties of water in a slit between two moving graphene walls under Couette flow conditions. A range of different slit widths and velocity strain rates are considered. It is shown that under the sub-nanometer confinement, water loses its rotational symmetry of a Newtonian fluid. In such conditions, water transforms into ice, where the atomistic structure is completely insensitive to the applied shear force and which behaves like a frozen slab sliding between the graphene walls. This leads to the shear viscosity increase, although not as dramatic as the normal force increase that contributes to the increased friction force reported in previous experimental studies. On the other end of the spectra, for flows at large velocity strain rates in moderate to large slits between the graphene walls, water is in the liquid state and reveals a shear thinning behavior. In this case, water exhibits a constant slip length on the wall, which is typical of liquids in the vicinity of hydrophobic surfaces.
Can Amphipod Behavior Help to Predict Chronic Toxicity of Sediments?

ABSTRACT Amphipods are widely used in both acute and chronic (sub-lethal) sediment tests. Acute sediment tests provide relatively rapid results, but may fail to detect moderately toxic contaminants that are bound to the sediment, whereas chronic life-cycle tests are rarely performed as they are time consuming and expensive. Observations during chronic testing of oil-contaminated sediment suggested that there may be a link between the behavior of the marine amphipod Corophium volutator and reduction in growth rate. Behavior tests were performed with six individual amphipods per treatment using sediment spiked with weathered Forties oil with burrowing time, re-emergence from sediment, and activity prior to burrowing as endpoints. Further behavior tests were used to predict the chronic toxicity of sediments spiked with three crude oils each with a dominant unresolved complex mixture of hydrocarbons (UCM). The effect of sediment type on behavior was also investigated. The results suggested that although the behavior test could not be used alone as a viable alternative to sediment toxicity tests, it could prove useful as an adjunct to acute tests, and help select sediments that deserve further investigation.
SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis

At the surge of the coronavirus disease 2019 (COVID-19) pandemic, we detected and identified six functional domains (I to VI) in the SARS-CoV-2 3a protein. Our analysis showed that the functional domains were linked to virulence, infectivity, ion channel formation, and virus release in SARS-CoV-2 3a. Our study also revealed the functional importance of conserved domains across the species barrier. Observations reported in this study merit experimental confirmation. ABSTRACT The effect of the rapid accumulation of nonsynonymous mutations on the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not yet known. The 3a protein is unique to SARS-CoV and is essential for disease pathogenesis. Our study aimed at determining the nonsynonymous mutations in the 3a protein in SARS-CoV-2 and determining and characterizing the protein’s structure and spatial orientation in comparison to those of 3a in SARS-CoV. A total of 51 different nonsynonymous amino acid substitutions were detected in the 3a proteins among 2,782 SARS-CoV-2 strains. We observed microclonality within the ORF3a gene tree defined by nonsynonymous mutations separating the isolates into distinct subpopulations. We detected and identified six functional domains (I to VI) in the SARS-CoV-2 3a protein. The functional domains were linked to virulence, infectivity, ion channel formation, and virus release. Our study showed the importance of conserved functional domains across the species barrier and revealed the possible role of the 3a protein in the viral life cycle. Observations reported in this study merit experimental confirmation. IMPORTANCE At the surge of the coronavirus disease 2019 (COVID-19) pandemic, we detected and identified six functional domains (I to VI) in the SARS-CoV-2 3a protein. Our analysis showed that the functional domains were linked to virulence, infectivity, ion channel formation, and virus release in SARS-CoV-2 3a. Our study also revealed the functional importance of conserved domains across the species barrier. Observations reported in this study merit experimental confirmation.
Formation of a DNA triple helical structure at BOLF1 gene of human herpesvirus 4 (HH4) genome

Abstract Eukaryotic genomes contain a large number of pyrimidine-purine rich regions and such regions can assume varied DNA conformations, including triple-stranded structures. These structures have fascinated scientists because of their considerable therapeutic applications. These structures have also profound implications in the field of nanotechnology as they can be used to develop DNA-based nanostructures and materials. Therefore, for any application, it is important to understand the formation of triplex structures, both in quantitative and qualitative terms. A combination of gel electrophoresis, UV-thermal denaturation and circular dichroism (CD) spectroscopy was used to investigate the formation of inter- as well as intramolecular triplex, in pyrimidine motif at BOLF1 gene of human herpesvirus 4 (HH4) genome. This gene codes for inner tegument protein, which plays crucial roles in viral replication. The said oligopurine•oligopyrimidine duplex was targeted via a designed triple helix forming oligopyrimidine nucleotide (TFO) in intermolecular as well as intramolecular fashion. Our studies revealed that intramolecular triplex formation takes place at acidic as well as at neutral pH; whereas low pH is required for its intermolecular version. This comparative study between inter- and intramolecular triplex allowed us to demonstrate that intramolecular structure is more stable to its intermolecular counterpart. Numerous models for mono-, bi- and trimolecular structures adopted by these DNA sequences have been suggested. This report adds to our existing knowledge about DNA triple helical structures. Graphical Abstract Communicated by Ramaswamy H. Sarma
Mexico: Lessons learned from the 2009 pandemic that help us fight COVID-19

In April 2009, Mexican, American, and Canadian authorities announced a novel influenza that became the first pandemic of the century. We report on lessons learned in Mexico. The Mexican Pandemic Influenza Preparedness and Response Plan, developed and implemented since 2005, was a decisive element for the early response. Major lessons-learned were the need for flexible plans that consider different scenarios; the need to continuously strengthen routine surveillance programs and laboratory capacity and strengthen coordination between epidemiological departments, clinicians, and laboratories; maintain strategic stockpiles; establish a fund for public health emergencies; and collaboration among neighboring countries. Mexico responded with immediate reporting and transparency, implemented aggressive control measures and generous sharing of data and samples. Lessons learned induced changes leading to a better response to public health critical events.
Espécies de Culicoides (Diptera; Ceratopogonidae) e hospedeiros potenciais em área de ecoturismo do Parque Nacional dos Lençóis Maranhenses, Brasil

Richness, relative abundance, and blood food source of Culicoides species were studied in rural and urban areas in Barreirinhas Brazilian tourist center, Maranhao State, in Lencois Maranhenses National Park area. Insects were collected in peridomiciliary environment using HP light traps placed about 1.5 m above the floor, from 6:00 pm to 6:00 am, in the years 2004 to 2007. The effort was 1,440 h. A total of 7,964 individuals belonging to 13 species were caught. The most abundant ones were Culicoides filariferus (30.7%), C. ignacioi (24.6%), C. insignis (13.8%), C. leopoldoi (12.8%), C. boliviensis (9.9%), C. foxi (4%), and C. paucienfuscatus (3.2%). The others were 1% of sampling. Culicoides sucked blood of mammals (54.3%, including humans, 11.2%) and birds (31.9%), more abundant in rural area where the average of catches was 878.9 specimens per locality compared to 18 specimens per locality in urban area. The high wealth and abundance of Culicoides species, and humans and domestic animals as blood hosts, have indicated future entomological studies are necessary to determine whether the tourism, one of the main local economic activities, has affected habitats and changed the community structure of those insects.