Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographic and Ecological Dimensions of Host Plant-Associated Genetic Differentiation and Speciation in the Rhagoletis cingulata (Diptera: Tephritidae) Sibling Species Group

Ascertaining the causes of adaptive radiation is central to understanding how new species arise and come to vary with their resources. The ecological theory posits adaptive radiation via divergent natural selection associated with novel resource use; an alternative suggests character displacement following speciation in allopatry and then secondary contact of reproductively isolated but ecologically similar species. Discriminating between hypotheses, therefore, requires the establishment of a key role for ecological diversification in initiating speciation versus a secondary role in facilitating co-existence. Here, we characterize patterns of genetic variation and postzygotic reproductive isolation for tephritid fruit flies in the Rhagoletis cingulata sibling species group to assess the significance of ecology, geography, and non-adaptive processes for their divergence. Our results support the ecological theory: no evidence for intrinsic postzygotic reproductive isolation was found between two populations of allopatric species, while nuclear-encoded microsatellites implied strong ecologically based reproductive isolation among sympatric species infesting different host plants. Analysis of mitochondrial DNA suggested, however, that cytoplasmic-related reproductive isolation may also exist between two geographically isolated populations within R cingulata. Thus, ecology associated with sympatric host shifts and cytoplasmic effects possibly associated with an endosymbiont may be the key initial drivers of the radiation of the R. cingulata group.
Looking for Asia’s Security Dilemma

In “Racing toward Tragedy? China’s Rise, Military Competition in the Asia Paciac, and the Security Dilemma,” Adam Liff and John Ikenberry claim that “a number of recent developments suggest that the region is ripe for, or may already be experiencing, severe security dilemma–driven dynamics, even arms races. ”1 They portray China’s rise as the main cause of this dilemma and assert that states must adopt measures to reduce military competition in the region while they still can. I applaud Liff and Ikenberry for the policy relevance of their research, but their fundamental claim about the prevalence of severe military competition in the Asia Paciac region does not match the empirical reality. The real puzzle is why over the last thirty years Asian countries have shown a surprising lack of interest in boosting their military expenditures in response to China’s massive increases, whether these expenditures are measured in absolute or proportional terms, and whether they are measured over the past generation or the last few years.
Efficacy and Safety of Vedolizumab Subcutaneous Formulation in a Randomized Trial of Patients With Ulcerative Colitis.

BACKGROUND & AIMS Maintenance treatment with vedolizumab, a monoclonal antibody that inhibits the gut-selective α4β7 integrin, is administered intravenously. Some patients might prefer a subcutaneous formulation of vedolizumab for maintenance treatment. Vedolizumab SC was investigated as maintenance treatment in patients with moderately to severely active ulcerative colitis (UC). METHODS We performed a phase 3, double-blind, double-dummy trial, at 141 sites in 29 countries, from December 18, 2015 through August 21, 2018. Patients with moderately to severely active UC received open-label treatment with intravenous vedolizumab 300 mg at weeks 0 and 2. At week 6, patients with clinical response were randomly assigned maintenance treatment with subcutaneous vedolizumab (108 mg) every 2 weeks, intravenous vedolizumab 300 mg every 8 weeks, or placebo. The primary endpoint was clinical remission at week 52, defined as a total Mayo score of 2 or lower and no subscore greater than 1. RESULTS Among 216 patients randomly assigned to groups, clinical remission at week 52 was achieved by 46.2%, 42.6%, and 14.3% of patients in the subcutaneous vedolizumab, intravenous vedolizumab, and placebo groups, respectively (subcutaneous vedolizumab vs placebo: Δ32.3%; 95% CI, 19.7%-45.0%; P<.001). The subcutaneous vedolizumab group also had greater endoscopic improvement and durable clinical response at week 52 compared with placebo (both P<.001). The incidence of injection-site reactions was more frequent in patients given subcutaneous vedolizumab (10.4%) than intravenous vedolizumab (1.9%) or placebo (0%); these were not treatment limiting, most were mild, and none resulted in discontinuation. Subcutaneous and intravenous vedolizumab safety profiles were otherwise similar. CONCLUSIONS Subcutaneous vedolizumab is effective as maintenance therapy in patients with moderately to severely active UC who had a clinical response to intravenous vedolizumab induction therapy. It has a favorable safety and tolerability profile. ClinicalTrials.gov no: NCT02611830; EudraCT 2015-000480-14.
Analysis of distance-based protein structure prediction by deep learning in CASP13

This paper reports the CASP13 results of distance-based contact prediction, threading and folding methods implemented in three RaptorX servers, which are built upon the powerful deep convolutional residual neural network (ResNet) method initiated by us for contact prediction in CASP12. On the 32 CASP13 FM (free-modeling) targets with a median MSA (multiple sequence alignment) depth of 36, RaptorX yielded the best contact prediction among 46 groups and almost the best 3D structure modeling among all server groups without time-consuming conformation sampling. In particular, RaptorX achieved top L/5, L/2 and L long-range contact precision of 70%, 58% and 45%, respectively, and predicted correct folds (TMscore>0.5) for 18 of 32 targets. Although on average underperforming AlphaFold in 3D modeling, RaptorX predicted correct folds for all FM targets with >300 residues (T0950-D1, T0969-D1 and T1000-D2) and generated the best 3D models for T0950-D1 and T0969-D1 among all groups. This CASP13 test confirms our previous findings: (1) predicted distance is more useful than contacts for both template-based and free modeling; and (2) structure modeling may be improved by integrating alignment and co-evolutionary information via deep learning. This paper will discuss progress we have made since CASP12, the strength and weakness of our methods, and why deep learning performed much better in CASP13.
A novel organic mineral complex prevented high fat diet-induced hyperglycemia, endotoxemia, liver injury and endothelial dysfunction in young male Sprague-Dawley rats

The prevalence of metabolic syndrome (MetSyn) has risen 35% since 2012 and over two-thirds of Americans exhibit features characterizing this condition (obesity, dyslipidemia, hyperglycemia, insulin resistance and/or endothelial dysfunction). The aim of this study was to evaluate the effects of a novel dietary supplemental organic mineral complex (OMC) on these risk factors in a rodent model of MetSyn. Six-week old male Sprague-Dawley rats were fed either standard chow or a high-fat diet (HFD) composed of 60% kcal from fat for 10 weeks. Rats were also treated with OMC in their drinking water at either 0 mg/mL (control), 0.6 mg/mL, or 3.0 mg/mL. The HFD-treated rats exhibited significantly increased body mass (p<0.05), epididymal fat pad mass (p<0.001), waist circumference (p = 0.010), in addition to elevations in plasma endotoxins (p<0.001), ALT activity (p<0.001), fasting serum glucose (p = 0.025) and insulin concentrations (p = 0.009). OMC did not affect body weight or adiposity induced by the HFD. At the higher dose OMC significantly blunted HFD-induced hyperglycemia (p = 0.021), whereas both low and high doses of OMC prevented HFD-induced endotoxemia (p = 0.002 and <0.001, respectively) and hepatocyte injury (ALT activity, p<0.01). Despite evidence of oxidative stress (elevated urinary H2O2 p = 0.032) in HFD-fed rats, OMC exhibited no demonstrable antioxidative effect. Consistent with prior studies, mesenteric arteries from HFD rats had more uncoupled eNOS (p = 0.006) and iNOS protein expression (p = 0.027) in addition to impaired endothelium-dependent vasodilation that was abrogated by the high dose of OMC (p<0.05). This effect of OMC may be attributed to the high nitrate content of the supplement. These findings suggest that the OMC supplement, particularly at the higher dose, ameliorated several risk factors associated with MetSyn via a non-antioxidant-dependent mechanism.
Does parental concern about their child’s future risk of overweight vary by their ethnic background? Cross-sectional analysis of a national cohort study

Objectives Children from South Asian ethnic backgrounds are at increased risk of obesity and its associated future health risks; however, evidence is lacking as to whether parental concern about their child’s future overweight risk varies by ethnic background. We hypothesised that parents of 5-year-old children from South Asian backgrounds would be more likely to express such concerns. Design Cross-sectional. Setting UK. Participants 15 039 singleton 5-year-old Millennium Cohort Study participants (48.9% girls; 86.7% White). Primary outcome measure Parent-reported concern (some/none) about future overweight risk. Methods We estimated the adjusted ORs (aORs) of some parental concern (ranging from a little to very concerned) by child’s ethnic background (reference group: White), adjusted for parent and child weight status, and child sex. Results Parents of girls from Pakistani (aOR 0.4; 95% CI 0.2 to 0.5), Bangladeshi (0.3; 0.2 to 0.5), Black African (0.5; 0.3 to 0.7) and Mixed (0.7; 0.5 to 0.99) ethnic backgrounds and of boys from Pakistani ethnic backgrounds (0.6; 0.4 to 0.9) were less likely to report concern about their child’s future overweight risk than parents of White girls and boys, respectively. Overweight (2.5; 2.2 to 2.8) and obesity (6.7; 5.7 to 7.9) in children, and overweight (1.4; 1.2 to 1.5) and obesity (1.9; 1.7 to 2.2) in parents, were associated with increased likelihood of concern. Conclusions Parents of children from South Asian ethnic backgrounds express less concern about their child’s future overweight risk. Qualitative studies are needed to understand the concerns of parents from different ethnic backgrounds to inform weight-management interventions in ethnically diverse populations.
Searchlight classification based on Amplitude of Low Frequency Fluctuation and functional connectivity in individuals with obsessive-compulsive symptoms

ABSTRACT Introduction Investigating obsessive-compulsive symptoms in subclinical populations provides a useful framework for understanding the early development of obsessive-compulsive spectrum disorders. The present study aimed to apply searchlight classification analysis on resting-state functional magnetic resonance imaging data to identify potential brain markers in subclinical individuals with obsessive-compulsive symptoms. Methods In this observational study, 40 college students with high obsessive-compulsive symptom scores and 40 with low obsessive-compulsive symptom scores were recruited from universities in China. We conducted searchlight classification and comparison analysis between the two groups based on Amplitude of Low Frequency Fluctuation (ALFF), fraction ALFF (fALFF) and resting-state functional connectivity using searchlight classification. Results We found that the highest accuracy rate in differentiating between the two groups was 85.00%. Significant discriminating features included the ALFF of the left medial superior frontal gyrus and the functional connectivity between the right thalamus and the bilateral medial superior frontal gyrus, and the right putamen, as well as the functional connectivity between the left caudate and the right insula. Conclusions These findings highlight the specific and distinguishing brain functional abnormalities associated with obsessive-compulsive symptoms.
Effects of antibacterial peptides on rumen fermentation function and rumen microorganisms in goats

Although many studies have confirmed that antimicrobial peptides (AMPs: PBD-mI and LUC-n) can be used as feed additives, there are few reports of their use in ruminants. The present study aimed to investigate the impact of AMPs on ameliorating rumen fermentation function and rumen microorganisms in goats. Eighteen 4-month-old Chuanzhong black goats were used in a 60-day experiment (6 goats per group). Group I was used as the control and was fed a basal diet, the group II were fed the basal diet supplemented with 2 g of AMPs [per goat/day] and group III were fed the basal diet supplemented 3 g of AMPs [per goat/day], respectively. Rumen fluid samples were collected at 0, 20 and 60 days. Bacterial 16S rRNA genes and ciliate protozoal 18S rRNA genes were amplified by PCR from DNA extracted from rumen samples. The amplicons were sequenced by Illumina MiSeq. Rumen fermentation parameters and digestive enzyme activities were also examined. Our results showed that dietary supplementation with AMPs increased the levels of the bacterial genera Fibrobacter, Anaerovibrio and Succiniclasticum and also increased the ciliates genus Ophryoscolex, but reduced the levels of the bacterial genera Selenomonas, Succinivibrio and Treponema, and the ciliate genera Polyplastron, Entodinium, Enoploplastron and Isotricha. Supplementation with AMPs increased the activities of xylanase, pectinase and lipase in the rumen, and also increased the concentrations of acetic acid, propionic acid and total volatile fatty acids. These changes were associated with improved growth performance in the goats. The results revealed that the goats fed AMPs showed improved rumen microbiota structures, altered ruminal fermentation, and improved efficiency regarding the utilization of feed; thereby indicating that AMPs can improve growth performance. AMPs are therefore suitable as feed additives in juvenile goats.
Next-generation sequencing for tumor mutation quantification using liquid biopsies

Abstract Background Non-small cell lung cancer (NSCLC) patients benefit from targeted therapies both in first- and second-line treatment. Nevertheless, molecular profiling of lung cancer tumors after first disease progression is seldom performed. The analysis of circulating tumor DNA (ctDNA) enables not only non-invasive biomarker testing but also monitoring tumor response to treatment. Digital PCR (dPCR), although a robust approach, only enables the analysis of a limited number of mutations. Next-generation sequencing (NGS), on the other hand, enables the analysis of significantly greater numbers of mutations. Methods A total of 54 circulating free DNA (cfDNA) samples from 52 NSCLC patients and two healthy donors were analyzed by NGS using the Oncomine™ Lung cfDNA Assay kit and dPCR. Results Lin’s concordance correlation coefficient and Pearson’s correlation coefficient between mutant allele frequencies (MAFs) assessed by NGS and dPCR revealed a positive and linear relationship between the two data sets (ρc = 0.986; 95% confidence interval [CI] = 0.975–0.991; r = 0.987; p < 0.0001, respectively), indicating an excellent concordance between both measurements. Similarly, the agreement between NGS and dPCR for the detection of the resistance mutation p.T790M was almost perfect (K = 0.81; 95% CI = 0.62–0.99), with an excellent correlation in terms of MAFs (ρc = 0.991; 95% CI = 0.981–0.992 and Pearson’s r = 0.998; p < 0.0001). Importantly, cfDNA sequencing was successful using as low as 10 ng cfDNA input. Conclusions MAFs assessed by NGS were highly correlated with MAFs assessed by dPCR, demonstrating that NGS is a robust technique for ctDNA quantification using clinical samples, thereby allowing for dynamic genomic surveillance in the era of precision medicine.
Flood Loss and Recovery Models for Residential Housing Stock : A Case Study of the 2013 Boulder , Colorado Floods

The recent catastrophic Boulder, Colorado flood of September, 2013, an event with a return period estimated as between 500 and 1,000 years [1], has shown how vulnerable a community can be to natural disasters and how the recovery of such a community is contingent on appropriate preparedness. Community resilience measurement and assessment are thus essential to support public policies and collective actions to reduce a disaster’s associated potential social disruptions and economic losses to the community and to improve community ability to adapt, withstand, and quickly recover from extreme hazard events. Among the essential ingredients for evaluating disaster resilience of communities are reliable and accurate models for the assessment of hazard-related losses for the built environment.
Exploring Students’ Descriptions of Mutation from a Cognitive Perspective Suggests How to Modify Instructional Approaches

Prior studies have shown that students have difficulty understanding the role of mutation in evolution and genetics. However, little is known about unifying themes underlying students’ difficulty with mutation. In this study, we examined students’ written explanations about mutation from a cognitive science perspective. According to one cognitive perspective, scientific phenomena can be perceived as entities or processes, and the miscategorization of processes as entities can lead to noncanonical ideas about scientific phenomena that are difficult to change. Students’ incorrect categorization of processes as entities is well documented in physics but has not been studied in biology. Unlike other scientific phenomena that have been studied, the word “mutation” refers to both the process causing a change in the DNA and the entity, the altered DNA, making mutation a relevant concept for exploration and extension of this theory. In this study, we show that, even after instruction on mutation, the majority of students provided entity-focused descriptions of mutation in response to a question that prompted for a process-focused description in a lizard or a bacterial population. Students’ noncanonical ideas about mutation occurred in both entity- and process-focused descriptions. Implications for conceptual understanding and instruction are discussed.
Magnetoresistance of Ultralow-Hole-Density Monolayer Epitaxial Graphene Grown on SiC

Silicon carbide (SiC) has already found useful applications in high-power electronic devices and light-emitting diodes (LEDs). Interestingly, SiC is a suitable substrate for growing monolayer epitaxial graphene and GaN-based devices. Therefore, it provides the opportunity for integration of high-power devices, LEDs, atomically thin electronics, and high-frequency devices, all of which can be prepared on the same SiC substrate. In this paper, we concentrate on detailed measurements on ultralow-density p-type monolayer epitaxial graphene, which has yet to be extensively studied. The measured resistivity ρxx shows insulating behavior in the sense that ρxx decreases with increasing temperature T over a wide range of T (1.5 K ≤ T ≤ 300 K). The crossover from negative magnetoresistivity (MR) to positive magnetoresistivity at T = 40 K in the low-field regime is ascribed to a transition from low-T quantum transport to high-T classical transport. For T ≥ 120 K, the measured positive MR ratio [ρxx(B) − ρxx(B = 0)]/ρxx(B = 0) at B = 2 T decreases with increasing T, but the positive MR persists up to room temperature. Our experimental results suggest that the large MR ratio (~100% at B = 9 T) is an intrinsic property of ultralow-charge-density graphene, regardless of the carrier type. This effect may find applications in magnetic sensors and magnetoresistance devices.
Sexually dimorphic responses of rats to fluoxetine in the forced swimming test are unrelated to the function of the serotonin transporter in the brain

Due to the prevalence of depression in women, female rats may be a better models for antidepressant research than males. In male rats, fluoxetine inhibited the serotonin (5‐hydroxytryptamine, 5‐HT) transporter (SERT) which is reducing the immobility time in the repeated forced swimming test (rFST). The performance of female rats in this test is unknown. In this study, responses of male and female rats in the rFST under chronic treatment with fluoxetine and the function of SERT in their brains were examined. Wistar rats received oral fluoxetine (females: 0, 1, 2.5, or 5 mg kg‐1 day‐1; males: 0 or 2.5 mg kg‐1 day‐1; in sucrose 10%, 1.5 ml/rat) 1 hr before the test daily for 12 days over the course of the rFST. rFST consisted of a 15 min pretest followed by 5 min sessions of swimming at 1 (test), 7 (retest 1), and 14 (retest 2) days later. SERT functioning was assessed by ex vivo assays of the frontal cortex and hippocampus of rats. Fluoxetine reduced immobility time of males in the rFST while it failed to do so in females. In vitro treatment with fluoxetine inhibited the uptake of 5‐HT of both sexes similarly, while in vivo chronic administration of fluoxetine failed to do so. In summary, rats responded to the chronic treatment with fluoxetine in a sexually dimorphic fashion during the rFST despite the functioning of SERT in their brains remaining equally unchanged. Hence, our data suggest that sexually dimorphic responses to fluoxetine in rFST may be unrelated to the function of SERT in rat brains.
Antenatal course and perinatal outcome after ultrasound detection of triple nuchal cord: a case series

Abstract Objective To determine the antenatal course and perinatal outcome of pregnancies in which a triple nuchal cord was detected prenatally by ultrasound. Methods Singleton pregnancies presenting for ultrasound evaluation after 24 weeks of gestation were routinely screened for the presence of nuchal cord loops using two-dimensional and color-Doppler ultrasound. Fetuses with more than two nuchal cord loops were identified from our fetal medicine database and their ultrasound reports and medical records were reviewed. Results During the study period from July 2014 to February 2019, 10 singleton fetuses with triple nuchal cord were identified, for a prevalence of 1 in 506 or 0.2%. No cases of more than three nuchal cord loops were detected. No predisposing factors were identified. Cases detected after 36 weeks (n = 4) delivered by cesarean section after 37 weeks and the diagnosis of triple nuchal cord was confirmed in all of them. Cases detected before 36 weeks (n = 6) underwent fetal surveillance. Among these cases, the umbilical cord unraveled itself from around the fetal neck in at least one loop in 83% of these cases. Overall, eight (80%) of the neonates were delivered by cesarean section for different reasons; in only two, the sole indication for cesarean delivery was the presence of the triple nuchal cord. All the infants had a good perinatal outcome, although one newborn infant was small for gestational age. Conclusions Ultrasound detection of triple nuchal cord during late pregnancy was associated with good perinatal outcomes. However, this prenatal finding was also associated with a high rate of cesarean section. In preterm pregnancies, multiple loops will reduce spontaneously in the majority of cases, so expectant management is indicated. In term pregnancies, the decision regarding the optimal timing and mode of delivery should be discussed with the parents taking into account the individual clinical scenarios.