Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and Temporal Organization of Odor-evoked Responses in a Fly Olfactory Circuit: Inputs, Outputs and Idiosyncrasies

How is sensory information routed through different types of neurons within a circuit, and do equivalent circuits in different individuals follow similar organizational principles? We examined this issue in the fruit fly olfactory system. Odor-evoked signals from sensory neurons (ORNs) triggered neural responses that were patterned over space and time in cholinergic ePNs and GABAergic iPNs within the antennal lobe. The dendritic-axonal (I/O) response mapping was complex and diverse, and axonal organization was region-specific (mushroom body vs. lateral horn). In the lateral horn, feed-forward excitatory and inhibitory axonal projections matched ‘odor tuning’ in a stereotyped, dorsal-lateral locus, but mismatched in most other locations. In the temporal dimension, ORN, ePN and iPN odor-evoked responses had similar encoding features, such as information refinement over time and divergent ON and OFF responses. Notably, analogous spatial and temporal coding principles were observed in all flies, and the latter emerged from idiosyncratic neural processing approaches. Highlights Consistency and idiosyncrasy both exist in ORN, ePN and iPN functional maps Signal transformations between different ePN compartments are complex and diverse Temporal decorrelation between stimuli happens in all three neuronal populations OFF responses that are orthogonal to ON responses emerge after odor termination
The Effect of post Chlamydia Trachomatis Infection treatment on Reactive Oxygen Species and Sperm Parameters of Infertile Men

Background Chlamydia trachomatis (CT) infection is often mentioned as a silent disease. Reactive oxygen species (ROS) can also cause Sperm apoptosis and have negative impact on Sperm parameters. The objectives of this study were to elucidate the association between Sperm parameters and ROS caused by CT infections resulting in male Infertility as well as evaluating the role of antibiotic therapy. Materials and methods A total of 848 infertile males having normal and abnormal Sperm parameters were included. After Semen sampling, the CT IgA were measured by Elisa and confirmed by Nested PCR. ROS was determined by Chemiluminescence. After treatment under the direct supervision of the private urologists. Then, the second Semen samples were taken and subjected to tests on Sperm parameters and ROS levels as assessed again. Results The levels of ROS and morphology were improved following the treatments (P<0.05). Antibiotic therapy due to CT infection, could reduce ROS, improve normal morphology and recover some of Semen parameters. Conclusions Our findings indicate that CT infection and Sperm parameters were associated with the rate of ROS in infertile men. However, after treatment, ROS value dropped allowing the recovery of certain Sperm parameters. Antibiotic therapy can improve some Semen quality parameters and treat the male Infertility. Reza Azmakan, rezaazmakan@yahoo.com, Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran, https://orcid.org/0000-0001-6718-3348.
Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

Background Despite their ecological and economical importance, conifers still have limited genomic resources, mainly due to the large size and complexity of their genomes. In addition, several of the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species the currently available transcriptomes are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Results Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris grown under natural conditions across five tissues: embryo, megagametophyte, needle, phloem, and vegetative bud. Compared to previous studies, we used a wider range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, and indication of tissue preferential upregulation or tissue preferential expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. The annotated genes were associated with a total of 84,498 GO terms, of which 1,834 had significant enrichment in different processes and functions, for example glyoxylate cycle in megagametophyte and defense response in needle. Even though most of the genes originating from the transcriptome do not have functional information in current biological databases, the tissue-specific patterns identified here provide valuable information about their potential functions for further studies. Conclusions The genes identified in this study will contribute to improve the annotation of the already available and forthcoming conifer genomes. This atlas of gene expression also provides ground to further the research in the areas of plant physiology, population genetics, and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.
Analysis of the immune response to sciatic nerve injury identifies efferocytosis as a key mechanism of nerve debridement

Sciatic nerve crush injury triggers sterile inflammation within the distal nerve and axotomized dorsal root ganglia (DRGs). Granulocytes and pro-inflammatory Ly6Chigh monocytes infiltrate the nerve first, and rapidly give way to Ly6Cnegative inflammation-resolving macrophages. In axotomized DRGs, few hematogenous leukocytes are detected and resident macrophages acquire a ramified morphology. Single-cell RNA-sequencing of injured sciatic nerve identifies five macrophage subpopulations, repair Schwann cells, and mesenchymal precursor cells. Macrophages at the nerve crush site are molecularly distinct from macrophages associated with Wallerian degeneration. In the injured nerve, macrophages “eat” apoptotic leukocytes, a process called efferocytosis, and thereby promote an anti-inflammatory milieu. Myeloid cells in the injured nerve, but not axotomized DRGs, strongly express receptors for the cytokine GM-CSF. In GM-CSF deficient (Csf2-/-) mice, inflammation resolution is delayed and conditioning-lesion induced regeneration of DRG neuron central axons is abolished. Thus, carefully orchestrated inflammation resolution in the nerve is required for conditioning-lesion induced neurorepair.
The Influence of the COVID-19 Outbreak on the Lifestyle of Older Patients With Dementia or Mild Cognitive Impairment Who Live Alone

Background: Under the COVID-19 outbreak, the Japanese government has strongly encouraged individuals to stay at home. The aim of the current study was to clarify the effects of the COVID-19 outbreak on the lifestyle of older adults with dementia or mild cognitive impairment (MCI) who live alone. Methods: Seventy-four patients with dementia or MCI aged ≥65 years, who regularly visited the dementia clinic of the Department of Psychiatry, Osaka University Hospital, were recruited in this study. The patients were divided into two groups according to their living situation: living alone group (n = 12) and living together group (n = 62). Additionally, the spouses of patients aged ≥65 years were assigned to the healthy control group (n = 37). Subjects' lifestyle changes were evaluated between April 8 and 28, 2020. Results: No subjects with acquaintances or relatives were infected with COVID-19 within the study period. The proportion of subjects who reduced going out in the living alone group, living together group and healthy control group was 18.2, 52.5, and 78.4%, respectively. The proportion of subjects who went out less frequently was significantly lower in both the living alone (p < 0.01) and living together (p < 0.05) groups than in the healthy control group. Conclusion: Most patients with dementia or MCI who live alone did not limit their outings or activities during the COVID-19 outbreak. Regular monitoring for potential COVID-19 infection in people living alone with dementia is vital for their safety and well-being.
Effects of Oral Drugs on Coronary Microvascular Function in Patients Without Significant Stenosis of Epicardial Coronary Arteries: A Systematic Review and Meta-Analysis of Coronary Flow Reserve

Objective: This study aims to investigate the impact of cardiovascular medications on the coronary flow reserve (CFR) in patients without obstructive coronary artery disease (CAD). Methods: We searched PubMed, EMBASE, and Cochrane databases from inception to 15 November 2019. Studies were included if they reported CFR from baseline to follow-up after oral drug therapy of patients without obstructive CAD. Data was pooled using random-effects modeling. The primary outcome was change in CFR from baseline to follow-up after oral drug therapy. Results: A total of 46 studies including 845 subjects were included in this study. Relative to baseline, the CFR was improved by angiotensin-converting enzymes (ACEIs), aldosterone receptor antagonists (ARBs) [standard mean difference (SMD): 1.12; 95% CI: 0.77–1.47], and statins treatments (SMD: 0.61; 95%CI: 0.36–0.85). Six to 12 months of calcium channel blocker (CCB) treatments improved CFR (SMD: 1.04; 95% CI: 0.51–1.58). Beta-blocker (SMD: 0.24; 95% CI: −0.39–0.88) and ranolazine treatment (SMD: 0.31; 95% CI: −0.39–1.01) were not associated with improved CFR. Conclusions: Therapy with ACEIs, ARBs, and statins was associated with improved CFR in patients with confirmed or suspicious CMD. CCBs also improved CFR among patients followed for 6–12 months. Beta-blocker and ranolazine had no impact on CFR.
Plumage coloration follows Gloger's rule in a ring species

Animal coloration is expected to differ between populations in different habitats according to Gloger's rule, with darker animals found in more humid, vegetated or warmer environments. Yet despite considerable support across the globe, the mechanisms behind this biogeographical rule are currently still unclear. Exploiting a ring species with plumage coloration from crimson to pale yellow, we test Gloger's rule and the mechanisms behind phenotypic divergence.
Enteric Viruses Co-infection with Giardiasis among Diarrheal Children in Diyala Province - Iraq

Mixed infections of enteric viruses and parasite can infected the human alimentary canal and quite complex physiological changes can result from such infection. To study the association between enteric viruses and giardiasis among diarrheal children as well as to clearly the relationship with Giardia lamblia genotypes in Diyala province, Iraq. Descriptive cross sectional study was conducted in Al-Batool Teaching Hospital for Maternity and Children in Baqubah city, during the period from June 2017 till November 2017. One hundred and sixty stool samples were collected from children with gastroenteritis using a clean and dry container. Samples, screened for rotavirus, adenovirus, astrovirus and norovirus using Cer Test Biotec, and G. lamblia by ELISA kits.The positive G. lamblia samples were further analyzed by nested polymerase chain reaction. Rotavirus was detected in 20%, adenovirus in 18.75% and norovirus in 13.75% while no positive result with astrovirus. G. lamblia were detected in 42 cases (26.25%), amplification triose phosphate isomerase (tpi) gene was successful in 28/42 (66.66%) samples, 8 (28.57%) contained genotype A and 20 (71.43%) samples contained genotype B. The majority of infected children were males less than five years old. Rotavirus infection rate amongst children in Diyala appears to be relatively higher than other enteric viruses. Co-infection with G. lamblia type B have important role.
An Efficient and Robust Antenna Combined with Electromagnetic Band-Gap Structure for Wearable Medical Application

A low-profile and robust inversely E-shaped antenna (IESA) combined with electromagnetic band-gap (EBG) is introduced for wearable medical application at 2.4 GHz. It has an overall size of 46×46×2.4 mm3. The EBG presented in this research is to isolate the antenna from the body. Thus, the performance of the antenna is not affected by the body. Contrarily, it reveals better performance compared to antenna in free space. The numerical and experiment results show that the integrated design shows good performance under bending and loading the human body. Moreover, the gain and the bandwidth were improved by 7.8 dBi and 27%, respectively. In addition, the SAR values were complied with standard. The reduction is more than 90.
Ossículos do moinho gástrico de cinco espécies de trichodactylidae (crustacea: decapoda: brachyura)

O estomago dos crustaceos decapodes esta dividido em tres regioes: esofago, câmara cardiaca e câmara pilorica, e possui um complexo muscular e nervoso no qual um conjunto de musculos estriados efetua os movimentos dos elementos esqueleticos do chamado moinho gastrico. Esse moinho gastrico consiste em um conjunto de elementos esqueleticos calcificados e um conjunto de musculos estriados que trabalham juntos para quebrar e moer grandes particulas de alimento dentro da câmara cardiaca do estomago. Esse conjunto esqueletico e composto pelos seguintes ossiculos: mesocardiaco, pterocardiaco, pilorico, exopilorico, zigocardiaco, propilorico e urocardiaco. Com o objetivo de testar se a atual hipotese de classificacao supragenerica da familia Trichodactylidae pode ser corroborada por caracteres morfologicos dos ossiculos gastricos, foram descritos os ossiculos do moinho gastrico de 25 individuos, entre machos e femeas adultos e jovens pertencentes a cinco especies: Trichodactylus fluviatilis (Trichodactylinae), Dilocarcinus pagei e Moreirocarcinus laevifrons (Dilocarcinini), e Sylviocarcinus pictus e Valdivia serrata (Valdiviini). Para a preparacao do material, os caranguejos foram dissecados, e seus estomagos submersos por um periodo de 24 horas em formol, posteriormente fervidos a 100◦C por 60 minutos numa solucao de hidroxido de potassio (KOH) e alizarina-vermelha com a finalidade de macerar todo o tecido do estomago e corar os ossiculos, respectivamente . A analise foi realizada com o auxilio de estereoscopio optico, e as ilustracoes dos estomagos e seus ossiculos individualizados foram feitas com o auxilio de câmara clara acoplada ao estereoscopio optico. Foi possivel reconhecer 48 ossiculos nas cinco especies estudadas, e entre eles foi possivel identificar diferencas significativas em nove ossiculos: ossiculos zigocardiaco, pre-pectineal, pectineal, subdentado, urocardiaco, mesopilorico posterior, anterior inferior pilorico, pilorico e pro-pilorico. De acordo com caracteristicas de determinadas regioes desses nove ossiculos, verificou-se que os agrupamentos resultantes sao consistentes com a atual proposta de classificacao de Trichodactylidae. A descricao de caracteres morfologicos internos podera contribuir para uma visao mais completa das relacoes intrafamiliares, concorrendo para uma delimitacao mais precisa da posicao sistematica de Trichodactylidae.
Comprehensive analysis of potential immunotherapy genomic biomarkers in 1,000 Chinese patients with cancer

Background Tumor mutation burden (TMB), DNA mismatch repair deficiency (dMMR), microsatellite instability (MSI), and PD-L1 amplification (PD-L1 AMP) may predict the efficacy of PD-1/PD-L1 blockade. In this study, we aimed to characterize the distributions of these biomarkers in over 1,000 Chinese patients with cancer. Methods TMB, MSI, dMMR, and PD-L1 AMP were determined based on whole-exome sequencing of tumor/blood samples from > 1,000 Chinese patients with cancer. Results Incidence rates among 953 Chinese patients with cancer showing high TMB (TMB-H), high MSI (MSI-H), dMMR and PD-L1 AMP were 35%, 4%, 0.53% and 0.04%, respectively. We found higher rates of TMB-H among hepatocellular carcinoma, breast cancer, and esophageal cancer patients than was reported for The Cancer Genome Atlas data. Lung cancer patients with EGFR mutations had significantly lower TMB values than those with wild-type EGFR, and increased TMB was significantly associated with dMMR in colorectal cancer (CRC). The frequency of tumors with MSI-H was highest in CRC (14%) and gastric cancer (4%). PD-L1 AMP occurred most frequently in lung squamous cell carcinoma (14.3%) and HER2-positive breast cancer (8.8%). Most MSI-H and dMMR cases exhibited TMB-H, but the overlap among the other biomarkers was low. Conclusion While MSI and dMMR are associated with higher mutational loads, correlations between TMB-H and other biomarkers, between MSI-H and dMMR, and between PD-L1 AMP and other biomarkers were low, indicating different underlying causes of the four biomarkers. Thus, it is recommended that all four biomarkers be assessed for certain cancers before administration of PD-1/PD-L1 blockade treatment.
Modélisation multi-échelles du comportement de l'eau et des ions dans les argiles

La prevision de l'evolution des dechets radioactifs lors d'un stockage en couche geologique argileuse profonde necessite une bonne comprehension du transport de l'eau et des ions dans l'argile. Leur diffusion dans ce milieu poreux et charge est decrite par des parametres empiriques, comme le coefficient de distribution (Kd) qui rend compte des interactions avec les surfaces minerales. Notre travail a porte sur la pertinence de ce concept et sa definition a partir de processus microscopiques. Nous avons d'abord modelise la contribution ionique aux proprietes dielectriques des argiles, et propose une determination de Kd par spectroscopie dielectrique. Nous avons ensuite calcule par simulations microscopiques (Monte-Carlo et dynamique moleculaire) les enthalpies libres et enthalpies d'echange ionique pour les ions alcalins, qui controlent Kd et ses variations avec la temperature T. Les resultats pour le cesium sont en bon accord avec des mesures de microcalorimetrie et de Kd en fonction de T. Apres avoir contribue au developpement d'une nouvelle methode de simulation sur reseau (Lattice Fokker-Planck), nous l'avons utilisee pour etablir un lien explicite entre la dynamique microscopique des ions et le modele de diffusion-reaction qui sous-tend la notion de Kd. Enfin, nous avons etudie par simulation de dynamique moleculaire la cinetique d'echange d'eau et d'ions entre les particules d'argile (porosite interfoliaire) et la porosite extra-particulaire. Les resultats confirment les hypotheses generalement admises selon lesquelles l'eau et les cations peuvent explorer toute la porosite, tandis que les anions sont exclus des espaces interfoliaires.
GWAS analysis combined with QTL mapping identify CPT3 and ABH as genes underlying dolichol accumulation in Arabidopsis

Dolichols (Dols), ubiquitous components of living organisms, are indispensable for cell survival. In plants, as well as other eukaryotes, Dols are crucial for posttranslational protein glycosylation, aberration of which leads to fatal metabolic disorders in humans. Until now, the regulatory mechanisms underlying Dol accumulation remain elusive. In this report, we have analyzed the natural variation of the accumulation of Dols and six other isoprenoids between 120 Arabidopsis thaliana accessions. Subsequently, by combining QTL and GWAS approaches, we have identified several candidate genes involved in the accumulation of Dols, polyprenols, plastoquinone, and phytosterols. The role of two genes implicated in the accumulation of major Dols in Arabidopsis – the AT2G17570 gene encoding a long searched for cis-prenyltransferase (CPT3) and the AT1G52460 gene encoding an alpha-beta hydrolase (ABH) – is experimentally confirmed. These data will help to generate Dol-enriched plants which might serve as a remedy for Dol-deficiency in humans.
Whole genome sequencing of Indonesian dengue virus isolates using next-generation sequencing

Indonesia is a tropical country and hyperendemic for dengue. The disease prevalently affected Indonesian and it caused high morbidity and substantial economic burden. This vector-borne viral disease is caused by infection of dengue viruses (DENVs), which are the member of Flaviviridae family. While most of dengue studies in Indonesia focused on the epidemiology, the clinical aspects, the vectors, and to certain extent the virology, there were still gaps in the DENVs genomic aspects. Considering their high mutation rate, the DENVs were known for their high genetic diversity and it might affect the characteristics of the viruses. Comprehensive DENV genomic data were thus important for many aspects of disease management, including virus surveillance, pathogenesis, diagnostics, antiviral drug design, and vaccine development. We established in this study a method for DENV whole genome sequencing using the advanced Next-Generation Sequencing (NGS) and Nextera XT DNA library preparation kit, coupled with simplified bioinformatic analysis methods. The Indonesian DENVs from four serotypes were isolated from patients’ sera, while library was prepared from enriched templates and sequenced using Illumina NGS. Our study highlighted the potential of a robust NGS method in producing whole genome sequence of DENVs, which would be important for future dengue studies.
How acupressure could influence self-efficacy of Infertile Women Undergoing Assisted Reproductive Technologies: A Qualitative Study

Background & aim: Infertility-related stress and anxiety can negatively affect the therapeutic outcome through directly influencing the physiological functions of the body. Also, improved self-efficacy of infertile women results in greater emotional stability and more persistence in treatment. The present study aimed to explore the perceptions and experiences of self-efficacy in infertile women who received acupressure during in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI). Methods: This qualitative study was conducted in Milad Infertility Center, Mashhad, Iran, from September 2015 to August 2016, using conventional content analysis. The study population consisted of 30 female candidates for IVF/ICSI treatment, who had completed acupressure therapy, the data of whom were extracted from a clinical trial. Out of 30 females, 26 cases were willing to participate in the study. The data were collected through in-depth and semi-structured interviews and analyzed in MAXQDA (version 10) software based on Elo and Kyngas approach (2008) through three phases of preparation, organization, and reporting. Results: Based on the results, two themes were obtained from the experiences of infertile women regarding the impact of acupressure on their infertility self-efficacy. These two themes included the improvement of the negative attitudes towards infertility and ability to deal with infertility treatment process. Conclusion: We argue that acupressure can improve the sense of self-efficacy in infertile women regarding their attitude toward infertility and treatment issues. Further studies are suggested on the influence of acupressure on various aspects of infertility.