Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley.

Meiotic recombination rates vary considerably between species, populations, and individuals. The genetic exchange between homologous chromosomes plays a major role in evolution by breaking linkage between advantageous and deleterious alleles in case of introgressions. Identifying recombination rate modifiers is thus of both fundamental and practical interest to understand and leverage variation in meiotic recombination rates. We investigated recombination rate variation in a large intraspecific hybrid population (named HEB-25) derived from a cross between domesticated barley and 25 wild barley accessions. We observed quantitative variation in total crossover number with a maximum of a 1.4-fold difference between subpopulations and increased recombination rates across pericentromeric regions. The meiosis-specific ɑ-kleisin cohesin subunit REC8 was identified as a candidate gene influencing crossover number and patterning. Furthermore, we quantified wild barley introgression patterns and revealed how local and genome-wide recombination rate variation shapes patterns of introgression. The identification of allelic variation in REC8 in combination with the observed changes in crossover patterning suggest a difference in how chromatin loops are tethered to the chromosome axis resulting in reduced crossover suppression across pericentromeric regions. Local and genome-wide recombination rate variation is shaping patterns of introgressions and thereby directly influences the consequences of linkage drag.
Genome-wide DNA methylation differences and polychlorinated biphenyl (PCB) exposure in a US population

ABSTRACT Exposure to polychlorinated biphenyls (PCBs), an endocrine-disrupting compound, is ubiquitous despite decades-old bans on the manufacture and use of PCBs. Increased exposure to PCBs is associated with adverse health consequences throughout life, including type 2 diabetes and cancer. PCB exposure is also associated with alterations in epigenetic marks and gene transcription, which could lead to adverse health outcomes, but many of these are population-specific. To further investigate the association between PCB and epigenetic marks, DNA methylation was measured at 787,684 CpG sites in 641 peripheral blood samples from the Michigan Polybrominated Biphenyl (PBB) Registry. 1345 CpGs were associated with increased total PCB level after controlling for age, sex, and 24 surrogate variables (FDR < 0.05). These CpGs were enriched in active promoter and transcription associated regions (p < 0.05), and in regions around the binding sites for transcription factors involved in xenobiotic metabolism and immune function (FDR < 0.05). PCB exposure also associated with proportions of CD4T, NK, and granulocyte cell types, and with the neutrophil to lymphocyte ratio (NLR) (p < 0.05), and the estimated effect sizes of PCB on the epigenome were correlated with the effect sizes previously reported in an epigenome-wide study of C-reactive protein (r = 0.29; p = 2.22e-5), supporting previous studies on the association between PCB and immune dysfunction. These results indicate that PCB exposure is associated with differences in epigenetic marks in active regions of the genome, and future work should investigate whether these may mediate the association between PCB and health consequences.
Comparison of the Sensititre YeastOne antifungal method with the CLSI M27-A3 reference method to determine the activity of antifungal agents against clinical isolates of Candida spp.

Background and aim Infections caused by Candida species are significantly increasing today, and invasive Candida infections are generally associated with high mortality. Early diagnosis and identification of Candida spp. is important for the determination of antifungal agents that will be used for treatment. The aim of the present study was to provide a better regimen for Candida infections in the future. Materials and methods The Sensititre YeastOne (SYO) method was compared with The Clinical Laboratory Standards Institute (CLSI) reference broth microdilution (BMD) testing method. Endpoints of minimal inhibitory concentrations (MICs) were determined for both methods. Results By using both methods, MIC values of micafungin, caspofungin, voriconazole, and fluconazole were lower than amphotericin B. The values obtained with the SYO method were in high categorical agreement for ecinocandins and amphotericin B. The results of voriconazole and fluconazole were in low categorical agreement. The categorical agreement between the SYO and the BMD results at 24 h was 82.1% for VORI and 98.4% for AMB. Values obtained with SYO method for all antifungal agents were in high essential agreement with the data of the CLSI reference BMD method. The essential agreement between the SYO and the BMD results at 24 h was 94.0% for MFG and 99.0% for AMB. Conclusions The SYO method was ready-to use, so it appeared to be easier and more efficient for Candida isolates.
SEXUAL DIFFERENCES IN THE POST-BREEDING MOVEMENTS AND HABITATS SELECTED BY WESTERN TOADS (BUFO BOREAS) IN SOUTHEASTERN IDAHO

We used radio-telemetry to study the movements and habitat use of Western toads (Bufo boreas) in the Targhee National Forest in southeastern Idaho. Eighteen toads (10 male and 8 female) that bred in a seasonally flooded pond, were fitted with radio-transmitters, tracked, and their movements mapped and analyzed with global positioning and geographic information systems. We also analyzed their patterns of habitat selection at micro- and macro-scales by comparing sites used by toads with randomly selected sites. After breeding, two male and six female toads left the breeding pond and used terrestrial habitats extensively. Male and female toads showed different patterns of movement and habitat use, although all toads seemed to behave in ways that reduced loss of body water (e.g., such as traveling on nights of high humidity). Male toads traveled shorter distances from the pond than females (581 ± 98 m and 1105 ± 272 m, respectively). Female toads used terrestrial habitats extensively and were selective of cover types (e.g., shrub) that provided greater protection from dehydration. Female toads also preferred certain habitat edges and open forests over forests with closed canopies or clearcuts. Information from this study can assist land managers in establishing protective buffers and managing forests for the protection of toad populations.
Distribution of certain soil inhabiting chytrid and chytridiaceous species related to some physical and chemical factors

Most ecological studies of chytrids and chytridiaceous fungi in soils are primarily distributional, and autecological information for particular species is scant. In this study the distribution of 11 species, Schizochytrium aggregatum, Thraustochytrium roseum, Chytriomyces hyalinus, Rhizophlyctis harderi, Rhizophydium sp. (utriculare? ), R. sphaerocarpum, R. carpophilum, R. sphaerotheca, Phlyctochytrium chaetiferum, P. palustre, and P. reinboldtae, is numerically expressed by an index (DII) derived from occurrence and frequency for 19 habitats. Mean values of various environmental parameters—pH, organic matter, bulk density, osmolarity, Ca2+, Mg2+, and Na+—are calculated for each habitat, and linear correlations of DII against means of the environmental factors of each habitat are calculated for each species. Also the range, mean, and standard deviation of chemical and physical parameters at sites where each species occurs are calculated. By these methods some autecological facts appear for each species. B.
Different brain profiles in children with prenatal alcohol exposure with or without early adverse exposures

Prenatal alcohol exposure (PAE) can alter brain development and impact mental health outcomes, and often occurs in conjunction with postnatal adversity (e.g., maltreatment). However, it is unclear how postnatal adverse exposures may moderate mental health and brain outcomes in children with PAE. T1‐weighted and diffusion magnetic resonance imaging were obtained from 66 participants aged 7–16 years. Twenty‐one participants had PAE and adverse postnatal exposures (PAE+), 12 had PAE without adverse postnatal exposures (PAE−), and 33 were age‐ and gender‐matched controls unexposed to either prenatal alcohol or postnatal adversity. Internalizing and externalizing mental health symptoms were assessed using the Behavioral Assessment System for Children II, Parent‐Rating Scale. ANCOVAs were used to compare mental health symptoms, limbic and prefrontal cortical volumes, and diffusion parameters of cortico‐limbic white matter tracts between groups, and to assess brain‐mental health relationships. Both PAE groups had worse externalizing behavior (higher scores) than controls. The PAE− group had lower fractional anisotropy (FA) in the bilateral cingulum and left uncinate fasciculus, and smaller volumes in the left anterior cingulate cortex than controls and the PAE+ group. The PAE− group also had higher mean diffusivity (MD) in the left uncinate than the PAE+ group, and smaller right anterior cingulate and superior frontal gyrus volumes than controls. These findings show different brain structure and mental health symptom profiles in children with PAE with and without postnatal adversity, highlighting the need to consider adverse postnatal exposures in individuals with PAE.
Repair of pulmonary artery sling with tracheal and intracardiac defects

Background Pulmonary artery sling is commonly associated with tracheal stenosis and intracardiac anomalies. While surgical repair is standardized, coexistent anomalies often determine outcomes. With the paucity of risk stratification, this study aimed to review our experience and stratify risk factors for the surgical outcome of complex pulmonary artery sling repair in the presence of airway or intracardiac lesions. Methods Seventy-nine consecutive children with pulmonary artery sling were evaluated retrospectively following surgical repair. Median age at surgery was 5 months (interquartile range 3–9). Surgical approaches included pulmonary artery sling alone (n = 10), pulmonary artery sling with tracheoplasty (n = 41), and pulmonary artery sling with both intracardiac and tracheal surgery (n = 28). Results There were 7 early (8.8%) deaths. Two patients after left pulmonary artery reimplantation needed revision of the anastomosis. The median intensive care and hospital stay were 11 (interquartile range 9.2–24.8) and 17.9 (interquartile range 4.3–19.8) days, and considerably longer when associated tracheal surgery (p = 0.002). Follow-up was complete in 66/69 and 3 (3.8%) children died late: 2.7, 10.2, and 17 months after surgery. Univariate analysis showed abnormal lung and coexisting structural heart disease as risk factors. Multivariate analysis revealed total cardiopulmonary bypass time as an independent predictor of overall mortality. Conclusion Complex pulmonary artery sling repair can be performed with a good surgical outcomes even when associated with airway malformations or structural heart diseases. Lung abnormality and longer cardiopulmonary bypass time as a surrogate marker of complex surgery, are possible risk factors.
Expression of interleukin 2 receptors on activated human B cells

Using anti-Tac, a monoclonal anti-interleukin 2 (IL-2) receptor antibody, we have explored the possibility that certain activated B cells display receptors for IL-2. Resting normal B cells and unselected B cell lines established from normal individuals were Tac antigen negative. In contrast, the cell surface Tac antigen expression was demonstrable on 6 of 10 B cell lines from patients with Burkitt's lymphoma, 5 of 6 B cell lines derived from patients with HTLV-I- associated adult T cell leukemia (including all four that had integrated HTLV-I into their genome), and on certain normal B cells activated with pokeweed mitogen. Furthermore, cloned Epstein-Barr virus- transformed B cell lines derived from Tac-positive normal B cells continued to express the Tac antigen in long-term cultures and manifested high affinity IL-2 receptors identified in binding studies with purified radiolabeled IL-2. The line 5B4 developed in the present study could be induced with purified JURKAT-derived or recombinant IL-2 to express a larger number of IL-2 receptors. Furthermore, the addition of IL-2 to the 5B4 B cell line augmented IgM synthesis, which could be blocked by the addition of anti-Tac. The size of the IL-2 receptors expressed on the cloned normal B cell lines was similar (53,000-57,000 daltons) to that of receptors on phytohemagglutinin-stimulated T cell lymphoblasts. Thus, certain malignant and activated normal B cells display the Tac antigen and manifest high affinity receptors for IL-2. These data suggest that IL-2 may play a role in the differentiation of activated B cells into immunoglobulin-synthesizing and -secreting cells.
Phosphorus transformations in the epilimnion of humic lakes: abiotic interactions between dissolved humic materials and phosphate

SUMMARY. 1. Sephadex gel filtration of filtered water from small, Finnish forest lakes demonstrated abiotic movement of 33P from added PO4 to two higher molecular weight fractions. This movement was most pronounced in waters with high humic content which also had high iron content. The two fractions which took up 13P had nominal molecular weights of > 100,000 and 10,000-20,000. 2. An equilibrium existed between free PO4 and the two fractions. However, one fraction, at least, appeared to exist in two phases, with one phase in rapid equilibrium with free PO4 but the other in only slow equilibrium. 3. Additions of ferric iron up to 1 mg Fe l−1 to the filtered lake water stimulated movement from free PO4, provided high concentrations of humic materials were present. In the absence of humic materials even 0.1 mg Fe 1−1 would precipitate all added 33PO4. 4. The high molecular weight P was only partially reactive with standard molybdate reagents. Exposure of the high molecular weight P to sunlight caused a small release of PO4 under the experimental conditions employed. 5. Possible implications for biological phosphorus demand of such sequestration of free PO4 by humic materials in combination with iron are discussed.
The Interaction of Temozolomide with Blood Components Suggests the Potential Use of Human Serum Albumin as a Biomimetic Carrier for the Drug

The interaction of temozolomide (TMZ) (the main chemotherapeutic agent for brain tumors) with blood components has not been studied at the molecular level to date, even though such information is essential in the design of dosage forms for optimal therapy. This work explores the binding of TMZ to human serum albumin (HSA) and alpha-1-acid glycoprotein (AGP), as well as to blood cell-mimicking membrane systems. Absorption and fluorescence experiments with model membranes indicate that TMZ does not penetrate into the lipid bilayer, but binds to the membrane surface with very low affinity. Fluorescence experiments performed with the plasma proteins suggest that in human plasma, most of the bound TMZ is attached to HSA rather than to AGP. This interaction is moderate and likely mediated by hydrogen-bonding and hydrophobic forces, which increase the hydrolytic stability of the drug. These experiments are supported by docking and molecular dynamics simulations, which reveal that TMZ is mainly inserted in the subdomain IIA of HSA, establishing π-stacking interactions with the tryptophan residue. Considering the overexpression of albumin receptors in tumor cells, our results propose that part of the administered TMZ may reach its target bound to plasma albumin and suggest that HSA-based nanocarriers are suitable candidates for designing biomimetic delivery systems that selectively transport TMZ to tumor cells.
Phylogeny of some Solanum species ( Solanaceae ) based on complete chloroplast genomes (cpDNA) and individual chloroplast genes

Chloroplast DNA sequences can be used to estimate phylogenetic relationships among plant taxa. There are many chloroplast sequences have been made available in public databases and these data have been used for phlyogenetic relationship and evolutionary processes. We used three Solanum species ( Solanum bulbocastanum , Solanum tuberosum and Solanum lycopersicum ) and Nicotiana tabacum as outgroup. We performed phylognetic analysis four species based on complete chloroplast DNA (cpDNA), matK coding region and trnL-trnF noncoding region by using Maximum Likelihood (ML), Neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) models. The all tree resulting from complete cpDNA clearly separated Solanum species with high bootstrap values and all the chloroplast segments clearly differentiated the genus Nicotiana tabacum from Solanum species. Tajima’s neutrality test revealed that the highest nucleotide diversity (0.01667) was observed in trnL-trnF non-coding region. UPGMA phylogenetic inference has been shown to be more robust to ML and NJ due to bootstrap values. Particularly, ML inference has lower phylogenetic resolution than UPGMA and NJ tree.
Post-traumatic stress symptoms in an Italian cohort of subjects complaining occupational stress

Abstract Objective Work-related stress presents a significant impact on work performance and physical health. It has been associated with the onset of a multitude of symptoms. The main aim of this investigation is to better understand the impact of post-traumatic stress symptomatology, using a specific self-assessment questionnaire, in subjects experiencing occupational stress with the rationale to address the variegated symptoms expressed by this particular population in a post-traumatic dimensional perspective. Methods Authors collected socio-demographic, occupational, and clinical data. They utilized Trauma and Loss Spectrum Self Report (TALS-SR), a questionnaire investigating post-traumatic stress symptoms. The population size was 345 subjects who presented at the Occupational Health Department of a university hospital over a 3 years period (2016–2018). Results Data analysis revealed 33.9% of subjects who met post-traumatic stress disorder (PTSD) criteria. Gender distribution of this set was (36.4% female, 31% male). A family history or personal history of mental disorders were related to higher scores in almost all TALS-SR domains and were related, respectively, to higher scores of criterion B “intrusion symptoms” (P = .014), criterion D “negative alterations in cognitions and mood” (P = .023), and criterion E “arousal” (P = .033) of PTSD. Differences in TALS-SR scores also emerged based on age and gender. Conclusions PTSD symptoms manifest at a significant level in those who experience work-related stress. Personal background of individuals, both in terms of family and personal history for mental disorders, seems to increase their vulnerability to develop post-traumatic stress symptoms. This study suggests the importance of evaluating occupational stress from a post-traumatic stress perspective also at an early stage.
Predictiveness of different preoperative risk assessments for postoperative bleeding after coronary artery bypass grafting surgery

Aim: Postoperative bleeding is a significant cause of morbidity and mortality in patients undergoing cardiac surgery. Studies have been conducted, and guidelines have been published regarding patient blood management and aiming to prevent blood loss in the perioperative period. Various bleeding risk assessments were developed for preoperative period. We aimed to examine the correlations of scoring systems in the literature with the amount of postoperative bleeding in patients undergoing first time coronary artery bypass graft surgery, and to show the most suitable preoperative bleeding risk assessment for coronary artery bypass graft patients. Methods: The study included 550 consecutive patients who underwent coronary artery bypass graft operation. The inclusion criteria were considered as patients to be older than 18 years old and to undergo elective or emergent myocardial revascularization using cardiopulmonary bypass. All variables required for scoring systems were recorded. The initial results of the study were determined as the amount of chest tube drainage, the use of blood products, the change in hematocrit level, reoperation due to bleeding, duration of ventilation, duration of intensive care unit stay, and hospital stay. Mortality which occurred during first 30 days after operation was considered as operative mortality. Operative mortality was accepted as the primary endpoint. Secondary endpoints were massive bleeding and high amount of transfusion. Results: Data were obtained from a series of 550 consecutive patients treated with isolated coronary artery bypass graft. It was seen that PAPWORTH and WILL-BLEED risk assessments responded better for E-CABG grade 2 and 3 bleeding compared to other risk assessments. TRACK, TRUST, and ACTA-PORT scales were found to have low ability to distinguish patients with E-CABG bleeding grade 2 and 3. Conclusion: Predicting postoperative bleeding and transfusion rates with preoperative risk scores in patients undergoing coronary artery bypass graft surgery will provide valuable information to physicians for establishing a proper patient blood management protocol and this will decrease excessive transfusions, unnecessary reoperations as well as improve postoperative outcomes.
Imidazole-based Synthetic Lipidoids for In Vivo mRNA Delivery into Primary T Lymphocytes.

Engineering T lymphocytes is an emerging approach in a variety of biomedical applications. However, delivering large biologics to primary T lymphocytes directly in vivo is technically challenging due to the low transfection efficacy. In this paper, we investigated a library of synthetic lipid-like molecules (lipidoids) for their capability of delivering mRNA into primary T lymphocytes both ex vivo and in vivo . We initially conducted a library screening with large structural variety of lipidoids ex vivo and identified imidazole-containing lipidoids that are particularly potent in T lymphocytes transfection. We further optimized lipidoid structures through constructing and screening a detailed lipidoid library containing imidazole or imidazole analogues to perform a structure-activity correlation analysis. Using the lead lipidoid as a delivery vehicle for Cre mRNA in vivo through intravenous injection, we obtained ~8.2% of gene recombination in mouse T lymphocytes.
Denitrification in sediment of lowland streams: regional and seasonal variation in Gelbaek and Rabis Baek, Denmark

Seasonal variations of denitrification activity and the relative importance of controlling factors like NO3− concentration and abundance of organic matter were determined in three different sediments from Danish lowland streams. In Gelbaek, which is a stream fed by NO3−-rich drainage water, highest denitrification activity (about 9 mmol N m−2 d−1) was observed in spring (May), together with high productivity and accumulation of benthic micro-algae on the sediment surface. During the summer, the diffusion flux of NO3− from the overlying water was a limiting factor for the decreasing denitrification activity. Both a non-vegetated, sandy sediment and a Batrachium peltatum-vegetated, organic-rich sediment were investigated in Rabis Baek, which is a stream fed primarily by NO3−-rich groundwater. In the sandy sediment, a denitrification maximum (about 4 mmol N m−2 d−1) was recorded in late spring (June), in combination with the bloom of benthic micro-algae. The availability of organic matter seemed to be the important limiting factor throughout the year. Denitrification also increased during the spring in the vegetated sediment, apparently in response to the growth of the plants; a maximum (about 11 mmol N m−2 d−1) was found in summer (July), immediately before the plants were cut to enhance water flow in the stream. Nitrification activity in the root zone of the plants was here the major NO3− source for denitrification, and the availability of NO3− limited the denitrification in this sediment.