Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphatidylethanol Levels in Postpartum Women and Their Newborns in Uruguay and Brazil.

BACKGROUND There is increasing interest in the development of newborn screening tests to identify children at risk of fetal alcohol spectrum disorder (FASD) in order to provide these children with early intervention. Phosphatidylethanol (PEth) has emerged as a potential universal newborn screening candidate. METHODS The aim of this report was to present the results of a study designed to compare PEth levels in 1,140 postpartum women and their newborn infants in Montevideo, Uruguay, and Sao Paulo, Brazil. Self-report alcohol use during pregnancy data was collected, along with both maternal and newborn dried blood spot samples for PEth analysis. RESULTS The average age and parity of the women in the sample were 26 years of age and 2.3 pregnancies. For the Uruguay sample (n = 611), 45.8% of postpartum women had PEth levels ≥ 8 ng/ml with a mean positive PEth of 43.6 ng/ml. In contrast, 86.8% of the newborns had PEth levels ≥ 8 ng/ml, with a mean positive PEth of 77.4 ng/ml. For the Brazil sample (n = 529), 33.2% of women had PEth levels ≥ 8 ng/ml with a mean positive PEth of 31 ng/ml. In contrast, 76.9% of the Brazil newborns had PEth levels ≥ 8 ng/ml and 43.9% with a mean positive PEth of 61.1 ng/ml. PEth levels were significantly higher in newborns compared with their postpartum mothers in both the Uruguay and Brazil samples. Self-reported third-trimester alcohol was 6% in the Uruguay sample and 9.1% in the Brazil sample compared with positive maternal PEth levels in 45.8% and 33.2%, respectively. CONCLUSIONS Clinicians may want to consider newborn PEth screening in high-risk populations where prenatal alcohol use is common. The mechanism underlying significantly higher PEth levels in newborns compared with their mothers is not known.
Pathology and Pathogenesis of SARS-CoV-2 Associated with Fatal Coronavirus Disease, United States

An ongoing pandemic of coronavirus disease (COVID-19) is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Characterization of the histopathology and cellular localization of SARS-CoV-2 in the tissues of patients with fatal COVID-19 is critical to further understand its pathogenesis and transmission and for public health prevention measures. We report clinicopathologic, immunohistochemical, and electron microscopic findings in tissues from 8 fatal laboratory-confirmed cases of SARS-CoV-2 infection in the United States. All cases except 1 were in residents of long-term care facilities. In these patients, SARS-CoV-2 infected epithelium of the upper and lower airways with diffuse alveolar damage as the predominant pulmonary pathology. SARS-CoV-2 was detectable by immunohistochemistry and electron microscopy in conducting airways, pneumocytes, alveolar macrophages, and a hilar lymph node but was not identified in other extrapulmonary tissues. Respiratory viral co-infections were identified in 3 cases; 3 cases had evidence of bacterial co-infection.
How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes.

RAS proteins are small membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the spatiotemporal properties of RAS through dimerization/clustering and signaling fidelity. To understand the effects of anionic lipids on key spatiotemporal properties of RAS, we dissected one millisecond of data from all-atom molecular dynamics simulations for KRAS4B on two model anionic lipid membranes that have 30% of POPS mixed with neutral POPC and 8% of PIP2 mixed with POPC. We unveiled the orientation space of KRAS4B, whose kinetics were slower and more distinguishable on the membrane containing PIP2 than the membrane containing POPS. Particularly, the PIP2-mixed membrane can differentiate a third kinetic orientation state from the other two known orientation states. We observed that each orientation state may yield different binding with a RAF kinase, which is required for activating the MAPK/ERK signaling pathway. However, an overall occluded probability, for which RAF kinases cannot bind KRAS4B, remain unchanged on the two different membranes. We identified rare fast diffusion modes of KRAS4B that appear coupled with orientations exposing to cytosolic RAF. Particularly on the membrane having PIP2, we found non-linear correlations between the orientation states and the conformations of the cationic farnesylated hypervariable region, which acts as an anchor in the membrane. Using diffusion coefficients estimated from the all-atom simulations, we quantified the effect of PIP2 and POPS on the KRAS4B dimerization via Green's function reaction dynamics simulations, in which the averaged dimerization rate is 12.5% slower on PIP2-mixed membranes.
Exhaustive Product Analysis of Three Benzene Discharges by Microwave Spectroscopy.

Using chirped and cavity microwave spectroscopies, automated double resonance, new high-speed fitting and deep learning algorithms, and large databases of computed structures, the discharge products of benzene alone, or in combination with molecular oxygen or nitrogen, have been exhaustively characterized between 6.5 and 26 GHz. In total, more than 3300 spectral features were observed; 88% of these, accounting for 97% of the total intensity, have now been assigned to 160 distinct chemical species and 60 of their variants (i.e. isotopic species and vibrationally excited states). Roughly 50 of the products are entirely new or poorly characterized at high resolution, including many heavier by mass than the precursor benzene. These findings provide direct evidence for a rich architecture of two- and three-dimensional carbon, and indicate that benzene growth, particularly formation of ring-chain molecules, occurs facilely under our experimental conditions. The present analysis also illustrates the utility of microwave spectroscopy as a precision tool for complex mixture analysis, irrespective of whether the rotational spectrum of a product species is known a priori or not. From this large quantity of data, for example, it is possible to determine with confidence the relative abundances of different product masses, but more importantly the relative abundances of different isomers with the same mass. The complementary nature of this type of analysis to traditional mass spectrometry is discussed.
Over 13,000 elements from a single bonebed help elucidate disarticulation and transport of an Edmontosaurus thanatocoenosis

Over twenty years of work on the Hanson Ranch (HR) Bonebed in the Lance Formation of eastern Wyoming has yielded over 13,000 individual elements primarily of the hadrosaurid dinosaur Edmontosaurus annectens. The fossil bones are found normally-graded within a fine-grained (claystone to siltstone) bed that varies from one to two meters in thickness. Almost all specimens exhibit exquisite preservation (i.e., little to no abrasion, weathering, and breakage), but they are disarticulated which, combined with our sedimentological observations, suggests that the bones were remobilized and buried after a period of initial decay and disarticulation of Edmontosaurus carcasses. Because of the large number of recovered fossil elements, we have been able to gain deeper insight into Edmontosaurus biostratigraphy including disarticulation and transport of skeletal elements. The most common postcranial elements in the bonebed are pubes, ischia, scapulae, ribs, and limb bones. By contrast, vertebrae, ilia, and chevrons are rare. The most common craniomandibular bones include dentaries, nasals, quadrates, and jugals, whereas the premaxillae, predentaries, and braincase bones are underrepresented. Thus, overall, chondrocranial and axial elements, as well as distal elements of the limbs, are distinctly underrepresented. We hypothesize that following decay and disarticulation, hydraulic winnowing removed the articulated sections (e.g., vertebral columns) and the small, distal-most elements before, or at the same time, the remaining bones were swept up in a subaqueous debris flow that generated the deposit. Comparison of the HR Bonebed with other widely dispersed Upper Cretaceous hadrosaurid-dominated bonebeds reveals many shared attributes, which suggests similar processes at work in the formation of these bonebeds across space and time. This in turn reflects similar behavior by populations of these species around the world resulting in similar modes of death, becoming interred in similar depositional settings.
Benthic Algal Resilience to Frequent Wet-Season Storm Flows in Low-Order Streams in the Australian Tropical Savanna

Abstract: Storm-flow disturbances are frequent during the wet season of Australian tropical savannas. We examined benthic algal resistance and resilience in open-canopy streams in the Daly River watershed. Storm flows occurred every 2 to 3 d at 1st- to 4th-order sites, with sharp rises and falls and relatively long periods of shallow, low-turbidity base flow. At a 5th-order site, storm-flow duration was longer and base flows were deeper and more turbid. We hypothesized that: 1) storm flow would dislodge benthic algal biomass, 2) baseflow biomass would be low, 3) taxon richness would be low, and 4) algal composition would be dominated by resistant algae with prostrate or erect growth forms or by fast growing colonizing algae. Hypothesis 1 was supported. Storm flows dislodged ~93% of epilithic biomass. Support for hypothesis 2 was equivocal. At the 5th-order site, sand mobility prevented establishment of benthic algae until seasonal flows receded. At the other sites, epilithon net growth rates were much greater than rates in some temperate streams. Benthic biomass was typical of temperate oligotrophic streams, but maximum biomass was typical of mesotrophic streams. We attributed the relatively rapid growth and high biomass to warm water temperatures (mean = 29°C, maximum = 36°C), high incident light, rapid algal nutrient uptake, loss of grazing invertebrates caused by storm flows, and physical impediments to fish access. Hypothesis 3 was not supported. Mean taxon richness was high because of the occurrence of rare taxa. Hypothesis 4 was not supported. Epilithic algal biomass was dominated by resistant filamentous chlorophytes. Epilithic algal resistance was similar to resistance in higher latitude streams, but resilience was greater. Epilithic algae potentially could supply autochthonous C to the Daly River and other tropical aquatic food webs.
La parure des Solutréens et des Magdaléniens anciens des Jamblancs

Cette courte etude de la parure dans les niveaux des Solutreens superieurs-Magdaleniens anciens des Jamblancs conclut a la permanence culturelle des formes choisies en parure. La selection des dents animales, des especes de coquillages et l'origine de ceux-ci qu'il faut chercher dans les faluns d'Aquitaine et sur les rivages atlantiques, la technique de percement particuliere a certaines dents et le decor simplifie laissent entrevoir le poids d'une forte tradition. D'etroites comparaisons peuvent s'etablir avec la parure des solutreo-magdaleniens du Pech de la Boissiere.
The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts

As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library construction with Juglans regia, walnut, as a model. Extracted walnuts were subjected to nano-liquid chromatography–mass spectrometry (n-LC-MS/MS), and spectra were searched against databases made from a six-frame translation of the genome (6FT), a transcriptome, and three proteomes. Searches against proteomic databases yielded a variable number of peptides (1156–1275), and only ten additional unique peptides were identified in the 6FT database. Searches against a transcriptomic database yielded results similar to those of the National Center for Biotechnology Information (NCBI) proteome (1200 and 1275 peptides, respectively). Performance of the transcriptomic database was improved via the adjustment of RNA-Seq read processing methods, which increased the number of identified peptides which align to seed allergen proteins by ~20%. Together, these findings establish a path towards the construction of robust proxy protein databases for tree nut species and other non-model organisms.
A Revised And Expanded Version Of The Turkish Childhood Trauma Questionnaire (CTQ-33): Overprotection-Overcontrol As Additional Factor

ABSTRACT This study was concerned with a culture-sensitive revision of the Turkish version of the Childhood Trauma Questionnaire (CTQ-28) and expansion of the instrument through integration of a dimension assessing overprotection – overcontrol (OP-OC). Participants (n = 783) were 37 dissociative and 78 non-dissociative and non-psychotic psychiatric outpatients, and 668 non-clinical people. They completed the revised and expanded version of the CTQ, Dissociative Experiences Scale, Beck Depression Scale, and Relationship Scales Questionnaire. A test-retest assessment was conducted on 25 non-clinical individuals. Among twenty-one alternative and the twenty-five original statements, the items of subsections were selected by correlations between item and item deleted total scores for each subset of original and alternative statements. The 33-item final version (CTQ-33) included five statements for each subsection including OP-OC and three denial items. The principal component analysis on items of the CTQ-33 with a varimax rotation yielded six factors including OP-OC. The inner consistency and the test-retest reliability were good. OP-OC correlated particularly with emotional abuse and neglect, and other types of trauma. There were significant correlations between CTQ-33 and depression, dissociation, and fearful attachment scores. The CTQ-33 differentiated psychiatric from non-clinical groups. The Turkish CTQ-33 is a reliable and valid instrument. OP-OC by caregivers may be as traumatic as other types of childhood adversities. Cross-cultural research would illuminate the significance of OP-OC beyond Turkish culture. The possibility of intergenerational transmission of trauma through OP-OC by fearful parents in and after times of cultural upheaval and political oppression should be considered for future research.
Repositioning PARP inhibitors for SARS‐CoV‐2 infection(COVID‐19); a new multi‐pronged therapy for acute respiratory distress syndrome?

Clinically approved PARP inhibitors (PARPi) have a mild adverse effect profile and are well tolerated as continuous daily oral therapy. We review the evidence that justifies the repurposing of PARPi to block the proliferation of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and combat the life‐threatening sequelae of coronavirus disease 2019 (COVID‐19) by several mechanisms. PARPi can effectively decrease IL‐6, IL‐1 and TNF‐α levels (key interleukins in SARS‐CoV‐2‐induced cytokine storm) and can alleviate subsequent lung fibrosis, as demonstrated in murine experiments and clinical trials. PARPi can tune macrophages towards a tolerogenic phenotype. PARPi may also counteract SARS‐CoV‐2‐induced and inflammation‐induced cell death and support cell survival. PARPi is effective in animal models of acute respiratory distress syndrome (ARDS), asthma and ventilator‐induced lung injury. PARPi may potentiate the effectiveness of tocilizumab, anakinra, sarilumab, adalimumab, canakinumab or siltuximab therapy. The evidence suggests that PARPi would benefit COVID‐19 patients and trials should be undertaken.
Genetic resources of wild barley in the near East: structure, evolution and application in breeding

Genetic diversity and structure of populations of the wild progenitor of barley, Hordeum spontaneum, from three countries, Israel, Turkey and Iran, in the Near East Fertile Crescent, are compared and contrasted. The analysis is based on electrophoretically discernible allozymic variation in proteins encoded by 27 shared loci in 2125 individuals representing 52 populations of wild barley. The results indicate that: (a) H. spontaneum in the Near East Fertile Crescent is very variable genetically; (b) genetic differentiation of populations includes some clinal but primarily regional and local patterns often displaying sharp geographic differentiation over short distances; (c) the average relative genetic differentiation (Gst) was 54% within populations, 39% among populations, and 8% between the three countries; (d) allele distribution is characterized by a high proportion of unique alleles (51%), and a high proportion of common alleles that are distributed either locally or sporadically; (e) discriminant analysis by allele frequencies successfully clustered wild barley of each of the three countries (96% correct classification); (f) a substantial portion of the patterns of allozyme variation in the wild gene pool is significantly correlated with the environment and is predictable ecologically, chiefly by a combination of humidity and temperature variables; (g) natural populations of wild barley are, on the average, more variable than two composite crosses and land races of cultivated barley. The spatial patterns and environmental correlates and predictors of genetic variation of H, spontaneum in the Fertile Crescent indicate that genetic variation in wild barley populations is not only rich but at least partly adaptive and predictable by ecology and allozyme markers. Consequently, conservation and utilization programmes should optimize sampling strategies by following the ecological-genetic factors and allozyme markers as effectively predictive guidelines.
American White Pelican Predation on Cui-ui in Pyramid Lake, Nevada

AbstractAnthropogenic changes to the Pyramid Lake–Truckee River ecosystem in Nevada are suspected to have altered the predator–prey balance between American white pelican Pelecanus erythrorhynchos and Cui-ui Chasmistes cujus. We estimated the loss of the adult Cui-ui population to pelican predation over a 13-year period by netting and tagging Cui-uis as they aggregated at the mouth of the Truckee River prior to their spawning migration into the Truckee River. Cui-ui access to the Truckee River typically required traversing a shallow delta (a foraging advantage for these American white pelicans). Dams and greater frequency of low stream flows also contributed to American white pelican foraging success. We used tag recoveries from Pyramid Lake's nesting colony of American white pelicans along with an experiment to estimate the chance of tag recovery within the colony to calculate the number of tagged fish taken by American white pelicans. We also used numbered tags to test whether there was a size preferenc.
Donated Human Milk as a Determinant Factor for the Gut Bifidobacterial Ecology in Premature Babies

Correct establishment of the gut microbiome is compromised in premature babies, with Bifidobacterium being one of the most affected genera. Prematurity often entails the inability to successfully breastfeed, therefore requiring the implementation of other feeding modes; breast milk expression from a donor mother is the recommended option when their own mother’s milk is not available. Some studies showed different gut microbial profiles in premature infants fed with breast milk and donor human milk, however, it is not known how this affects the species composition of the genus Bifidobacterium. The objective of this study was to assess the effect of donated human milk on shaping the gut bifidobacterial populations of premature babies during the first three months of life. We analyzed the gut bifidobacterial communities of 42 premature babies fed with human donor milk or own-mother milk by the 16S rRNA–23S rRNA internal transcriber spaces (ITS) region sequencing and q-PCR. Moreover, metabolic activity was assessed by gas chromatography. We observed a specific bifidobacterial profile based on feeding type, with higher bifidobacterial diversity in the human donor milk group. Differences in specific Bifidobacterium species composition may contribute to the development of specific new strategies or treatments aimed at mimicking the impact of own-mother milk feeding in neonatal units.
Gender Inequalities in Health and Their Effect on the Economic Prosperity Represented by the GDP of Selected Developed Countries—Empirical Study

The objective is to evaluate the relations between gender health inequalities and economic prosperity in the Organisation for Economic Co-operation and Development (OECD) countries. The groups included health indicators in the specification of men, women and gender inequalities: life expectancy, causes of mortality and avoidable mortality. The variable determining the economic prosperity was represented by the Gross Domestic Product (GDP). The analytical processing included descriptive analysis, analysis of differences and analysis of relationships. The regression analysis was presented as the main output of the research. Most of the significant gender differences in health showed a more positive outcome for women. It is possible to identify a certain relation between gender health inequalities and economic prosperity. If there is some reduction in gender inequalities in health, the economic prosperity will increase. The reduction seems to be more effective on the part of men than women. The output of the cluster analysis showed the relations of indicators evaluating the inequalities and the prosperity. The countries such as Luxembourg, Norway or Switzerland showed very positive outputs, on the other hand, the countries with a potential for the improvement are Lithuania, Latvia or Estonia. Overall, the policies should focus on reducing the inequalities in avoidable mortality as well as reducing the frequent diseases in younger people.
Genomic epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates from Ukraine, 2013–2018

Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major health threat compromising the gonorrhoea treatment globally. AMR surveillance including whole genome sequencing (WGS)‐based epidemiology provides ideal resolution to identify and describe AMR gonococcal clones, AMR determinants and populations, which can inform management guidelines and antimicrobial stewardship policies. Our aims were to, for the first time, elucidate the WGS‐based epidemiology and characterize AMR determinants of gonococcal strains spreading in Ukraine, 2013–2018. Gonococcal isolates (n = 150) from Ternopil and Dnipro, Ukraine (2013–2018), were subjected to AMR testing (Etest) for eight antimicrobials and WGS. Overall, 11.3% of isolates were resistant to ciprofloxacin, 6.0% to tetracycline, and 0.7% to benzylpenicillin. No isolates were resistant to azithromycin, spectinomycin, ceftriaxone, or cefixime, but one isolate was bordering resistance to both cephalosporins. Twenty‐five MLST STs, 50 NG‐MAST STs, and 34 NG‐STAR types were identified. The phylogenomic analysis revealed six main clusters, mostly associated with the internationally described multidrug‐susceptible gonococcal lineage. Resistance to ciprofloxacin was associated with GyrA S91F and ParC S87R mutations; tetracyclines with rpsJ V57M and tetM; penicillins with mosaic penA‐34.001 and β‐lactamase; mtrR; PorB1b G101D, and PBP1 L421P mutations. One isolate of the multidrug‐resistant NG‐MAST ST1407, MLST ST1901 was found, which was bordering resistance to ceftriaxone and cefixime. The antimicrobial susceptibility of gonococcal strains spreading in Ternopil and Dnipro, Ukraine, in 2013–2018 was surprisingly high. Continued and expanded gonococcal AMR surveillance, ideally including WGS, in Ukraine is essential. This could inform action plans and public health policies to control the spread of AMR gonococcal strains in Ukraine.