Miracle-dz/UniFAR-FTUs huggingface dataset:
Commercial integrated crop-livestock systems achieve comparable crop yields to specialized production systems: A meta-analysis

Production systems that feature temporal and spatial integration of crop and livestock enterprises, also known as integrated crop-livestock systems (ICLS), have the potential to intensify production on cultivated lands and foster resilience to the effects of climate change without proportional increases in environmental impacts. Yet, crop production outcomes following livestock grazing across environments and management scenarios remain uncertain and a potential barrier to adoption, as producers worry about the effects of livestock activity on the agronomic quality of their land. To determine likely production outcomes across ICLS and to identify the most important moderating variables governing those outcomes, we performed a meta-analysis of 66 studies comparing crop yields in ICLS to yields in unintegrated controls across 3 continents, 12 crops, and 4 livestock species. We found that annual cash crops in ICLS averaged similar yields (-7% to +2%) to crops in comparable unintegrated systems. The exception was dual-purpose crops (crops managed simultaneously for grazing and grain production), which yielded 20% less on average than single-purpose crops in the studies examined. When dual-purpose cropping systems were excluded from the analysis, crops in ICLS yielded more than in unintegrated systems in loamy soils and achieved equal yields in most other settings, suggesting that areas of intermediate soil texture may represent a “sweet-spot” for ICLS implementation. This meta-analysis represents the first quantitative synthesis of the crop production outcomes of ICLS and demonstrates the need for further investigation into the conditions and management scenarios under which ICLS can be successfully implemented.
Oocytes can efficiently repair DNA double-strand breaks to restore genetic integrity and protect offspring health

Significance An adequate supply of healthy oocytes is essential for female fertility. Oocytes that sustain even very low levels of DNA damage are killed, presumably because the damage is irreparable. Surprisingly, however, we show that when apoptosis is inhibited, oocytes can repair severe DNA damage via homologous recombination repair. The repair is highly efficient; it protects fertility and ensures the health and genetic integrity of offspring. These data implicate DNA repair as an additional quality control mechanism available within the female germ line. Female fertility and offspring health are critically dependent on an adequate supply of high-quality oocytes, the majority of which are maintained in the ovaries in a unique state of meiotic prophase arrest. While mechanisms of DNA repair during meiotic recombination are well characterized, the same is not true for prophase-arrested oocytes. Here we show that prophase-arrested oocytes rapidly respond to γ-irradiation–induced DNA double-strand breaks by activating Ataxia Telangiectasia Mutated, phosphorylating histone H2AX, and localizing RAD51 to the sites of DNA damage. Despite mobilizing the DNA repair response, even very low levels of DNA damage result in the apoptosis of prophase-arrested oocytes. However, we show that, when apoptosis is inhibited, severe DNA damage is corrected via homologous recombination repair. The repair is sufficient to support fertility and maintain health and genetic fidelity in offspring. Thus, despite the preferential induction of apoptosis following exogenously induced genotoxic stress, prophase-arrested oocytes are highly capable of functionally efficient DNA repair. These data implicate DNA repair as a key quality control mechanism in the female germ line and a critical determinant of fertility and genetic integrity.
Alterations of fecal microbiome characteristics by dietary soy isoflavone ingestion in growing pigs infected with porcine reproductive and respiratory syndrome virus.

Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important disease, and ingestion of soy isoflavones (ISF) may benefit PRRSV-infected pigs due to demonstrated anti-inflammatory and anti-viral properties. The objective of this study was to quantify effects of ISF consumption on fecal microbiome characteristics at different timepoints across a disease challenge and determine whether any changes, if present, elude to potential biological mechanisms for previously observed performance benefits. In total, 96 weaned barrows were group-housed in a Biosafety Level-2 containment facility and allotted to 1 of 3 experimental treatments that were maintained throughout the study: non-infected pigs receiving an ISF-devoid control diet (NEG, n=24), and infected pigs receiving either the control diet (POS, n=36) or that supplemented with total ISF in excess of 1,600 mg/kg (ISF, n=36). Following a 7-day adaptation, pigs were inoculated intranasally with either a sham-control (PBS) or live PRRSV (1×105 TCID50/mL, strain NADC20). Fecal samples were collected from 48 individual pigs at pre-infection (-2 days post-inoculation, DPI), peak-infection (10 DPI), post-infection (144 DPI) time-points. Extracted DNA was used to quantify fecal microbiota profiles via 16S bacterial rRNA sequencing. Differences in bacterial communities among diet groups were evaluated with principal co-ordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) using UniFrac distance matrices. Both unweighted and weighted UniFrac distances using QIIME 2. All other data were analyzed by one-way ANOVA performed on square root transformations using R. Across all time-points, only a few differences were observed due to ISF alone mainly in lowly abundant genera. The most notable differences observed was decreased relative abundance of Actinobacteria at 144 DPI between non-infected and infected treatments (P < 0.05), which is consistent with various dysbioses observed in other disease models. Our findings indicate that differences present were mainly due to PRRSV-infection alone and not strongly influenced by diet, which implies previously observed performance benefits conferred by dietary ISF are not likely due to changes in microbiome composition.
Neuroligin3 splice isoforms shape inhibitory synaptic function in the mouse hippocampus

Synapse formation is a dynamic process essential for the development and maturation of the neuronal circuitry in the brain. At the synaptic cleft, trans-synaptic protein–protein interactions are major biological determinants of proper synapse efficacy. The balance of excitatory and inhibitory synaptic transmission (E-I balance) stabilizes synaptic activity, and dysregulation of the E-I balance has been implicated in neurodevelopmental disorders, including autism spectrum disorders. However, the molecular mechanisms underlying the E-I balance remain to be elucidated. Here, using single-cell transcriptomics, immunohistochemistry, and electrophysiology approaches to murine CA1 pyramidal neurons obtained from organotypic hippocampal slice cultures, we investigate neuroligin (Nlgn) genes that encode a family of postsynaptic adhesion molecules known to shape excitatory and inhibitory synaptic function. We demonstrate that the NLGN3 protein differentially regulates inhibitory synaptic transmission in a splice isoform–dependent manner at hippocampal CA1 synapses. We also found that distinct subcellular localizations of the NLGN3 isoforms contribute to the functional differences observed among these isoforms. Finally, results from single-cell RNA-Seq analyses revealed that Nlgn1 and Nlgn3 are the major murine Nlgn genes and that the expression levels of the Nlgn splice isoforms are highly diverse in CA1 pyramidal neurons. Our results delineate isoform-specific effects of Nlgn genes on the E-I balance in the murine hippocampus.
Small mammals from the most radioactive sites near the chornobyl nuclear power plant

This study was designed to estimate the impact of pollution resulting from the meltdown of Reactor 4, Chornobyl, Ukraine, on the taxonomic diversity and abundance of small mammals in the surrounding area. Trap sites included the most radioactive areas within the 10-km exclusion zone, a site within the 30-km exclusion zone that received minimal radioactive pollution, and five sites outside of the 30-km exclusion zone. Within the exclusion zones, 355 specimens representing 11 species of small mammals were obtained, whereas 224 specimens representing 12 species were obtained from outside the exclusion zone. It is concluded that the diversity and abundance of the small-mammal fauna is not presently reduced at the most radioactive sites. Specimens from the most radioactive areas do not demonstrate aberrant gross morphological features other than enlargement of the spleen. Examination of karyotypes does not document gross chromosomal rearrangements.
Alteration in brain connectivity in patients with Dravet syndrome after vagus nerve stimulation (VNS): exploration of its effectiveness using graph theory analysis with electroencephalography

Objective. Vagus nerve stimulation (VNS) is a nonpharmacologic therapeutic option for patients who have pharmaco-resistant Dravet syndrome (DS). Plentiful efforts have been made for delivering VNS to DS patients, but its effectiveness still requires further verification. We investigated the effectiveness of the VNS treatment of DS patients using brain connectivity analysis with electroencephalography (EEG). Approach. Twenty pharmaco-resistant DS patients were selected to undergo VNS implantation and classified into responder and non-responder groups after 24 months post-VNS. The effect of VNS between 6 months pre- and 6, 12, and 24 months post-VNS in all patients, responders, and non-responders on four different frequency categories of four brain parameters were compared using resting-state EEG. Main results. In alpha and beta bands, all patients showed positive results for characteristic path length (CPL), global efficiency (GE), and transitivity after VNS treatment, and changes in betweenness centrality (BC) were not significant. The difference in transitivity between responders and non-responders is more pronounced than those in CPL and GE are, in both the alpha (p < 0.015) and beta (p < 0.001) bands. There was an obvious change in BC, especially in the alpha band, as the hubs tended to move from frontal lobe to parietal lobe for responders; however, there was no change for the non-responders. Significance. We investigated the alteration in brain connectivity of DS patients in alpha and beta bands during a long-term follow-up and found the responders have a decreased transitivity after the VNS treatment. Moreover, the hubs with high values in the alpha band tended to move from frontal lobe to parietal lobe for responders after VNS treatment.
CLINES IN THE GENETIC DISTANCE BETWEEN TWO SPECIES OF ISLAND LAND SNAILS :HOW 'MOLECULAR LEAKAGE' CAN MISLEAD US ABOUT SPECIATION

Two species of land snails, Partula taeniata and Partula suturalis , occur sympatrically on the island of Moorea in French Polynesia. The genetic distance between them varies clinally from north to south. Their extreme difference in the south is attributed to an invasion from the neighbouring island of Tahiti. Their genetic closeness in the north, despite large morphological and ecological differences, is attributed to ‘ molecular leakage’, convergence of the neutral and advantageous genes in the two species through occasional hybridization. Rates of hybridization as low as 1 in 100000 can render two species nearly homogeneous in their gene frequencies over periods of time that are short on an evolutionary scale, and therefore can completely mislead us about the phylogenetic history of the taxa concerned. In such circumstances the only valid phylogenetic information may be contained in genes that are kept distinct by natural selection.
Daily parenting of children with cerebral palsy: The role of daily child behavior, parents’ daily psychological needs, and mindful parenting

Abstract The purpose of this study was to advance the current understanding of the daily dynamics that are involved in raising a child with Cerebral Palsy (CP). Specifically, we examined the role of mindful parenting and of day-to-day variation in parents’ psychological needs and child behavior in explaining day-to-day variation in parents’ autonomy-supportive, psychologically controlling, and responsive parenting behavior. Parents (N = 58) of children with CP (Mage = 12.68 years) participated in a 7-day diary study. Multilevel analyses indicated that parents’ autonomy-supportive, psychologically controlling, and responsive behaviors fluctuate considerably between days. Further, daily fluctuations in both child behavior and parents’ own psychological needs were found to be associated with this daily variability in parenting. In addition, interindividual differences in mindful parenting were associated positively with parents’ responsiveness and negatively with psychologically controlling parenting across the week. These findings point towards the changeability of parenting behavior among parents of a child with CP and suggest that interventions targeting parenting behavior in the context of CP will be most effective when taking into account both the parents’ and the child's functioning.
The Amino-Acid Sequence of the α Subunit in Bovine Brain S-100a Protein

The brain specific S-100 protein is a mixture of two components S-100a and S-100b with a subunit composition αβ or β2 respectively. The amino acid sequence of the β subunit has been previously determined. This paper presents the sequence of the α subunit in the S-100a protein. The α subunit consists of 93 amino-acid residues and has a relative molecular mass of 10400. The sequence shows extensive homology (58%) with that of the β-subunit and shares an apparent calcium binding site in the C-terminal half of the molecule, suggesting a close evolutionary relationship between these subunits.
A clinically significant bronchodilator response in children: how should it be measured?

We thank F. Guezguez and H. Ben Saad for raising important questions on recommendations for assessing a bronchodilator response (BDR) in children. The authors summarise how recommended outcome measures and cut-offs for BDR in children vary between guidelines, and raise questions about our study [1]. More research is needed to evaluate the usefulness of diagnostic tests for asthma in children and cut-offs should be critically questioned and defined based on evidence from the patient population of interest https://bit.ly/33xjLVW
The effect of sediment type upon the position and depth at which byssal attachment occurs in Mytilus edulis

The effect of changes in particle size and sediment depth on byssal attachment was assessed in laboratory experiments. Mytilus edulis did not attach byssus pads to mud or silt less than 0·85 mm in diameter, but did attach pads to gravel. On gravel more pads were attached to the substrate (mean = 19·44 threads/mussel/week) than to other mussels in the group (mean = 7·34 threads/mussel/week). Because no byssal attachment to the finer substrates occurred and preference for other mussels in the groups rather than the plastic of the holding tank was shown, clumps, characteristic of mussel beds in the field, were formed. The clumps became increasingly well defined as the depth of the substrate increased. Few clumps were formed on the coarsest substrate as a result of preferential byssal attachment to gravel particles.
Association of Socioeconomic Status and Comorbidities with Racial Disparities during Kidney Transplant Evaluation.

BACKGROUND AND OBJECTIVES Black patients referred for kidney transplantation have surpassed many obstacles but likely face continued racial disparities before transplant. The mechanisms that underlie these disparities are unclear. We determined the contributions of socioeconomic status (SES) and comorbidities as mediators to disparities in listing and transplant. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We studied a cohort (n=1452 black; n=1561 white) of patients with kidney failure who were referred for and started the transplant process (2009-2018). We estimated the direct and indirect effects of SES (self-reported income, education, and employment) and medical comorbidities (self-reported and chart-abstracted) as mediators of racial disparities in listing using Cox proportional hazards analysis with inverse odds ratio weighting. Among the 983 black and 1085 white candidates actively listed, we estimated the direct and indirect effects of SES and comorbidities as mediators of racial disparities on receipt of transplant using Poisson regression with inverse odds ratio weighting. RESULTS Within the first year, 876 (60%) black and 1028 (66%) white patients were waitlisted. The relative risk of listing for black compared with white patients was 0.76 (95% confidence interval [95% CI], 0.69 to 0.83); after adjustment for SES and comorbidity, the relative risk was 0.90 (95% CI, 0.83 to 0.97). The proportion of the racial disparity in listing was explained by SES by 36% (95% CI, 26% to 57%), comorbidity by 44% (95% CI, 35% to 61%), and SES with comorbidity by 58% (95% CI, 44% to 85%). There were 409 (42%) black and 496 (45%) white listed candidates transplanted, with a median duration of follow-up of 3.9 (interquartile range, 1.2-7.1) and 2.8 (interquartile range, 0.8-6.3) years, respectively. The incidence rate ratio for black versus white candidates was 0.87 (95% CI, 0.79 to 0.96); SES and comorbidity did not explain the racial disparity. CONCLUSIONS SES and comorbidity partially mediated racial disparities in listing but not for transplant.
The -463G/A and -129G/A myeloperoxidase-encoding gene polymorphism in chronic obstructive pulmonary disease.

INTRODUCTION Neutrophils are involved in the pathogenesis of chronic obstructive pulmonary disease (COPD). Myeloperoxidase is an important bactericidal granulocytic enzyme. It is of interest to question whether or not the polymorphic variants of the myeloperoxidase-encoding gene are associated with the risk of developing COPD. MATERIAL AND METHODS The study determined the risk of COPD development in 186 COPD patients and 220 healthy subjects in the context of two selected polymorphic sites of the promoter region of the myeloperoxidase-encoding gene. RESULTS It has been demonstrated that the AA genotype of locus -463 in the myeloperoxidase-encoding gene increases the risk of developing COPD (OR: 2.87; CI: 1.651-4.997). This genotype also correlates with a higher gene expression in patients (0.56 ± 0.12 vs 0.31 ± 0.18 in patients with AG genotype and 0.29 ± 0.17, p < 0.01 in those with GG genotype). In healthy indivi-duals, the AA genotype was also characterized by increased expression of the myeloperoxidase-encoding gene (0.41 ± 0.16 vs 0.29 ± 0.15 for AG genotype, p < 0.01 and 0.25 ± 0.16 for GG genotype p < 0.01). Patients with the AA genotype had a significantly higher gene expression than healthy subjects with this genotype. CONCLUSIONS The polymorphic site -129 of the myeloperoxidase-encoding gene was unrelated to the development of COPD. The gene expression did not differ for the individual genotypes. Our studies indicate that the polymorphism of the myeloperoxidase--encoding gene may be related to chronic obstructive pulmonary disease.
Elbow flexion strength and contractile activity after partial ulnar nerve or intercostal nerve transfers for brachial plexus injuries

We compared the outcomes of 23 partial ulnar nerve and 15 intercostal nerve transfers for elbow flexion reconstruction in patients with C56 or C567 brachial plexus injuries using manual muscle power, dynamometric measurements of elbow flexion strength and electromyography. The range of elbow flexion and muscle strength recovery to Grade 3 or 4 were comparable between the two groups. The patients with C567 injuries had significantly stronger eccentric contraction after the partial ulnar nerve transfer than after the intercostal nerve transfer (p < 0.05). Electromyography of individual muscles demonstrated that the patients with partial ulnar nerve transfers were unable to voluntarily isolate biceps contraction and recruited forearm flexors and extensors. The patients after partial ulnar nerve transfer had significantly more activity of the forearm muscles during concentric elbow flexion than after intercostal nerve transfers (p < 0.05). We conclude that partial ulnar nerve transfers were superior to intercostal nerve transfers when assessed quantitatively with the dynamometer to evaluate elbow flexion, although simultaneous recruitment of forearm muscles may have contributed to the increased elbow flexion strength in the patients with the partial ulnar nerve transfer. Level of evidence: III
Colorectal Adenomas—Genetics and Searching for New Molecular Screening Biomarkers

Colorectal cancer (CRC) is a malignant disease with an incidence of over 1.8 million new cases per year worldwide. CRC outcome is closely related to the respective stage of CRC and is more favorable at less advanced stages. Detection of early colorectal adenomas is the key to survival. In spite of implemented screening programs showing efficiency in the detection of early precancerous lesions and CRC in asymptomatic patients, a significant number of patients are still diagnosed in advanced stages. Research on CRC accomplished during the last decade has improved our understanding of the etiology and development of colorectal adenomas and revealed weaknesses in the general approach to their detection and elimination. Recent studies seek to find a reliable non-invasive biomarker detectable even in the blood. New candidate biomarkers could be selected on the basis of so-called liquid biopsy, such as long non-coding RNA, microRNA, circulating cell-free DNA, circulating tumor cells, and inflammatory factors released from the adenoma into circulation. In this work, we focused on both genetic and epigenetic changes associated with the development of colorectal adenomas into colorectal carcinoma and we also discuss new possible biomarkers that are detectable even in adenomas prior to cancer development.
Structure–Function Analysis of the Herpes Simplex Virus Type 1 UL12 Gene: Correlation of Deoxyribonuclease Activityin Vitrowith Replication Function

Although the product of the UL12 gene of herpes simplex virus type 1 (HSV-1) has been shown to possess both exonuclease and endonuclease activities in vitro, and deletion of most of the gene within the viral genome results in inefficient production and maturation of infectious virions, the function of the deoxyribonuclease (DNase) activity per se in virus replication remains unclear. In order to correlate the in vitro and in vivo activities of the protein encoded by UL12, mutant proteins were tested for nuclease activity in vitro by a novel hypersensitivity cleavage assay and for their ability to complement the replication of a DNase null mutant, AN-1. Rabbit reticulocyte lysates programmed with wild-type UL12 RNA cleaved at the same sites cleaved by purified HSV-1 DNase, but distinct from those cleaved by DNase 1 or micrococcal nuclease. All mutants which lacked DNase activity in vitro also failed to complement the replication of AN-1 in nonpermissive cells. Likewise, all mutants which contained HSV-1 DNase activity, as detected by the hypersensitivity cleavage assay, were capable of complementing the replication of the DNase null mutant, though to varying extents. Of particular note was the d1-126 mutant protein, which, despite having the same specific activity as the wild-type enzyme in vitro, complemented the replication of AN-1 significantly less than the wild-type protein. The results suggest that DNase activity per se is required for efficient replication of HSV-1 in vivo. However, residues, including the N-terminal 126 amino acids, which are dispensable for enzymatic activity in vitro may facilitate the accessibility or activity of the protein in vivo.