Miracle-dz/UniFAR-FTUs huggingface dataset:
A Roadmap for Functional Structural Variants in the Soybean Genome

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.
Field Attraction of Carob Moth to Host Plants and Conspecific Females

Abstract The carob moth, Ectomyelois ceratoniae (Zeller; Lepidoptera: Pyralidae), is a devastating pest in high-value crops around the world. An efficient sex pheromone attractant is still missing for the management of this pest, because the major pheromone component is unstable. Host plant volatiles attract herbivore insects and have shown to have good potential to be exploited as alternatives or supplements to sex pheromones.To explore this possibility in carob moth, we assessed the attraction of moths to the volatiles of mature pistachio and different fruit stages of pomegranate, alone and in combination with virgin females, using sticky delta traps in pomegranate orchards of Iran. Traps baited with mature pomegranates, whether uncracked or cracked, infested or uninfested, caught significantly larger numbers of male and both mated and virgin female carob moths than unbaited traps. Traps baited with headspace extract of cracked pomegranate only caught mated females, while mature pistachio only attracted males. Pomegranate flowers, unripe pomegranate, and headspace extract of pistachio did not attract moths. Traps baited with cracked fruit caught more mated females than traps baited with uncracked fruit. Males were attracted similarly to traps baited with cracked-infested pomegranate as to traps baited with virgin females alone. Interestingly, the combination of cracked pomegranate and virgin female enhanced the attraction of virgin females.Together, our results show that volatiles from cracked pomegranates alone or in combination with female sex pheromone have great potential for application in pest management programs of carob moth.
A dynamic hurdle model for zero-inflated count data

ABSTRACT Excess zeros are encountered in many empirical count data applications. We provide a new explanation of extra zeros, related to the underlying stochastic process that generates events. The process has two rates: a lower rate until the first event and a higher one thereafter. We derive the corresponding distribution of the number of events during a fixed period and extend it to account for observed and unobserved heterogeneity. An application to the socioeconomic determinants of the individual number of doctor visits in Germany illustrates the usefulness of the new approach.
Interactive comment on “ Monitoring shipping emissions in the German Bight using MAX-DOAS measurements ” by André Seyler

General comment: This paper describes a 3 year series of multi axis DOAS measurements carried out from the German island Neuwerk, just south of the entry to the river Elbe. This is in the main ship channel of the port of Hamburg and the main aim of the measurements was to study these by observing UV and visible light horizontally towards the ship channel. The paper is well written, with good language and instructive graphs. The paper is a nice combination of measurements methodology and results paper. It shows the methodology to measure mixing ratios in a coastal places, together with ship plume measurements and some results about the effect of new IMO legislation. However, the OBJECTIVE and AIM should be declared more clearly in the text. The paper is also rather long, and I would recommend to shorten it, by removing sections which are outside the main scope of the paper. Forinstance merging and shortening sect 4.5 and 4.6 corresponding to mixing ratio measurements and comparisons. All in all, I believe the paper should be published, with some minor improvements, based on answering my specific comments below:
Expressive Speech Animation Synthesis with Phoneme‐Level Controls

This paper presents a novel data‐driven expressive speech animation synthesis system with phoneme‐level controls. This system is based on a pre‐recorded facial motion capture database, where an actress was directed to recite a pre‐designed corpus with four facial expressions (neutral, happiness, anger and sadness). Given new phoneme‐aligned expressive speech and its emotion modifiers as inputs, a constrained dynamic programming algorithm is used to search for best‐matched captured motion clips from the processed facial motion database by minimizing a cost function. Users optionally specify ‘hard constraints’ (motion‐node constraints for expressing phoneme utterances) and ‘soft constraints’ (emotion modifiers) to guide this search process. We also introduce a phoneme–Isomap interface for visualizing and interacting phoneme clusters that are typically composed of thousands of facial motion capture frames. On top of this novel visualization interface, users can conveniently remove contaminated motion subsequences from a large facial motion dataset. Facial animation synthesis experiments and objective comparisons between synthesized facial motion and captured motion showed that this system is effective for producing realistic expressive speech animations.
Therapeutic Hypothermia Reduces Oxidative Damage and Alters Antioxidant Defenses after Cardiac Arrest

After cardiac arrest, organ damage consequent to ischemia-reperfusion has been attributed to oxidative stress. Mild therapeutic hypothermia has been applied to reduce this damage, and it may reduce oxidative damage as well. This study aimed to compare oxidative damage and antioxidant defenses in patients treated with controlled normothermia versus mild therapeutic hypothermia during postcardiac arrest syndrome. The sample consisted of 31 patients under controlled normothermia (36°C) and 11 patients treated with 24 h mild therapeutic hypothermia (33°C), victims of in- or out-of-hospital cardiac arrest. Parameters were assessed at 6, 12, 36, and 72 h after cardiac arrest in the central venous blood samples. Hypothermic and normothermic patients had similar S100B levels, a biomarker of brain injury. Xanthine oxidase activity is similar between hypothermic and normothermic patients; however, it decreases posthypothermia treatment. Xanthine oxidase activity is positively correlated with lactate and S100B and inversely correlated with pH, calcium, and sodium levels. Hypothermia reduces malondialdehyde and protein carbonyl levels, markers of oxidative damage. Concomitantly, hypothermia increases the activity of erythrocyte antioxidant enzymes superoxide dismutase, glutathione peroxidase, and glutathione S-transferase while decreasing the activity of serum paraoxonase-1. These findings suggest that mild therapeutic hypothermia reduces oxidative damage and alters antioxidant defenses in postcardiac arrest patients.
Sweden, the first country to achieve the Joint United Nations Programme on HIV/AIDS (UNAIDS)/World Health Organization (WHO) 90‐90‐90 continuum of HIV care targets

The Joint United Nations Programme on HIV/AIDS (UNAIDS)/World Health Organization (WHO) 90‐90‐90 goals propose that 90% of all people living with HIV should know their HIV status, 90% of those diagnosed should receive antiretroviral therapy (ART), and 90% of those should have durable viral suppression. We have estimated the continuum of HIV care for the entire HIV‐1‐infected population in Sweden.
Double Diffeomorphism: Combining Morphometry and Structural Connectivity Analysis

The brain is composed of several neural circuits which may be seen as anatomical complexes composed of grey matter structures interconnected by white matter tracts. Grey and white matter components may be modeled as 3-D surfaces and curves, respectively. Neurodevelopmental disorders involve morphological and organizational alterations which cannot be jointly captured by usual shape analysis techniques based on single diffeomorphisms. We propose a new deformation scheme, called double diffeomorphism, which is a combination of two diffeomorphisms. The first one captures changes in structural connectivity, whereas the second one recovers the global morphological variations of both grey and white matter structures. This deformation model is integrated into a Bayesian framework for atlas construction. We evaluate it on a data-set of 3-D structures representing the neural circuits of patients with Gilles de la Tourette syndrome (GTS). We show that this approach makes it possible to localise, quantify, and easily visualise the pathological anomalies altering the morphology and organization of the neural circuits. Furthermore, results also indicate that the proposed deformation model better discriminates between controls and GTS patients than a single diffeomorphism.
Neighborhood Perceptions and Cumulative Impacts of Low Level Chronic Exposure to Fine Particular Matter (PM2.5) on Cardiopulmonary Health

Adverse perceptions of neighborhood safety, aesthetics and quality including access to resources can induce stress and may make individuals more sensitive to cardiopulmonary effects of air pollution exposure. Few studies have examined neighborhood perceptions as important and modifiable non-chemical stressors of the built environment that may exacerbate effects of air pollution on cardiopulmonary health outcomes, particularly among general population based cohorts. This study examined associations between low-level chronic exposure to fine particulate matter (PM2.5) and cardiopulmonary health, and the potential mediating or modifying effects of adverse neighborhood perceptions. Using data from the Survey of the Health of Wisconsin (SHOW), 2230 non-asthmatic adults age 21–74 were included in the analyses. The overall goals of this study were to assess if individuals who experience stress from neighborhood environments in which they live were more sensitive to low levels of fine particular matter (PM2.5 μg/m3). Demographic predictors of air pollution exposure included younger age, non-White race, lower education and middle class income. After adjustments, objective lung function measures (FEV1 and FEV1 to FVC ratio) were the only cardiopulmonary health indicators significantly associated with chronic three-year annual averages of PM2.5. Among all non-asthmatics, a ten unit increase in estimated three year annual average PM2.5 exposure was significantly associated with lower forced expiratory volume (L) in one second FEV1 (β = −0.40 μg/L; 95% CI −0.45, −0.06). Among all individuals, adverse perceptions of the neighborhood built environment did not appear to statistically moderate or mediate associations. However, stratified analysis did reveal significant associations between PM2.5 and lung function (FEV1) only among individuals with negative perceptions and increased reports of neighborhood stressors. These findings included individuals who felt their neighborhoods were poorly maintained (β = −0.82; 95% CI −1.35, −0.28), experienced stress from crime (β = −0.45; 95% CI −0.94, 0.04) or reported neighborhood is not well maintained (β = −1.13, CI −2.04, −0.24). These significant associations were similar for FEV1 to FVC ratio. Multi-pronged approaches addressing both neighborhood built environment aesthetics and air pollution regulation may be necessary to protect vulnerable and susceptible individuals and reduce persistent inequalities.
Understanding hierarchy and functions of bone using scanning x-ray scattering methods

Biological materials are often hierarchically structured from the nanometre to the macroscopic scale. Specific characterization methods are needed to characterize the structures at these different length scales. This chapter reviews, based on the example of bone, the use of X‐ray scattering methods to explore representative and quantitative structure information as well as structure–function relations in hierarchically structured biological materials. X‐ray scattering techniques are particularly well suited for the characterization of the form and ordering of organic as well as inorganic components in those materials. When nanometre‐sized structures are exposed to X‐rays, details on the internal material structure can be revealed by the analysis of the resulting interference patterns. Based on the example of bone, fundamental aspects of wide‐ and small‐angle X‐ray scattering (WAXS and SAXS) are discussed and examples how to apply these techniques are presented. By the use of scanning SAXS (sSAXS), i.e. moving the specimen step by step across a narrow X‐ray beam and collecting a SAXS pattern at each step, also specimen areas much larger than the beam size can be analysed. Furthermore, X‐ray scattering techniques can be combined with simultaneously performed mechanical experiments, which allows the investigation of the changes in structure resulting from external forces. To visualize the internal structure of biological materials also full‐field X‐ray methods are well suited. One example is X‐ray dark‐field imaging where the image contrast is formed through the mechanism of small‐angle scattering.
Is Firearm Threat in Intimate Relationships Associated with Posttraumatic Stress Disorder Symptoms Among Women?

In the context of intimate partner violence (IPV), firearms may be used to threaten, coerce, and intimidate. Yet, what little research exists on firearms among IPV victims has focused almost exclusively on homicide or near homicide. Thus, the deleterious health consequences of firearms more broadly remain unknown. The goals of the current study were (1) to document the prevalence of firearm threat in a community sample of female IPV victims, and (2) to identify the extent to which threat with a firearm, independent of other forms of IPV, is related to women's posttraumatic stress disorder (PTSD) symptom severity. Participants were 298 women who had been a victim in a criminal domestic violence case with a male intimate partner (Mage = 36.39 years; 50.0% African American; 51.3% unemployed). Retrospective data on firearm threat, fear of firearm violence, other IPV victimization (i.e., physical, psychological, and sexual), and PTSD symptoms were collected during in-person individual interviews. Approximately one-quarter of the sample (24.2%) experienced threat with a firearm during the course of their relationship, and 12.5% were afraid that their partners would use a firearm against them in the 30 days prior to the study interview. Firearm threat and fear of firearm violence emerged as significant and unique predictors of PTSD symptom severity, controlling for age and physical, psychological, and sexual IPV victimization severity. The findings underscore firearm threat as a key factor for identifying and intervening with criminal justice involved women who experience IPV.
Whole exome sequencing identifies mutations in 10% of patients with familial non-syndromic cleft lip and/or palate in genes mutated in well-known syndromes

Background Oral clefts, that is, clefts of the lip and/or cleft palate (CL/P), are the most common craniofacial birth defects with an approximate incidence of ~1/700. To date, physicians stratify patients with oral clefts into either syndromic CL/P (syCL/P) or non-syndromic CL/P (nsCL/P) depending on whether the CL/P is associated with another anomaly or not. In general, patients with syCL/P follow Mendelian inheritance, while those with nsCL/P have a complex aetiology and, as such, do not adhere to Mendelian inheritance. Genome-wide association studies have identified approximately 30 risk loci for nsCL/P, which could explain a small fraction of heritability. Methods To identify variants causing nsCL/P, we conducted whole exome sequencing on 84 individuals with nsCL/P, drawn from multiplex families (n=46). Results We identified rare damaging variants in four genes known to be mutated in syCL/P: TP63 (one family), TBX1 (one family), LRP6 (one family) and GRHL3 (two families), and clinical reassessment confirmed the isolated nature of their CL/P. Conclusion These data demonstrate that patients with CL/P without cardinal signs of a syndrome may still carry a mutation in a gene linked to syCL/P. Rare coding and non-coding variants in syCL/P genes could in part explain the controversial question of ‘missing heritability’ for nsCL/P. Therefore, gene panels designed for diagnostic testing of syCL/P should be used for patients with nsCL/P, especially when there is at least third-degree family history. This would allow a more precise management, follow-up and genetic counselling. Moreover, stratified cohorts would allow hunting for genetic modifiers.
Biogeosciences Effect of ocean acidification on marine fish sperm ( Baltic cod : Gadus morhua )

Ocean acidification, as a consequence of increasing marine pCO2, may have severe effects on the physiology of marine organisms. However, experimental studies remain scarce, in particular concerning fish. While adults will most likely remain relatively unaffected by changes in seawater pH, early life-history stages are potentially more sensitive – particularly the critical stage of fertilization, in which sperm motility plays a central role. In this study, the effects of ocean acidification (decrease of pHT to 7.55) on sperm motility of Baltic cod, Gadus morhua, were assessed. We found no significant effect of decreased pH on sperm speed, rate of change of direction or percent motility for the population of cod analyzed. We predict that future ocean acidification will probably not pose a problem for sperm behavior, and hence fertilization success, of Baltic cod.
Attenuation of Leukocytes Sequestration by Carbon Monoxide-Releasing Molecules: Liberated Carbon Monoxide in the Liver of Thermally Injured Mice

We sought to determine whether the CO-releasing molecules, ie, liberated CO, attenuates the leukocytes sequestration in the liver of thermally injured mice. Sixty-five mice were assigned to five groups in three respective experiments. In each experiment, mice in sham group (n = 7) and sham + CORM-2 group (n = 7) were underwent sham thermal injury, whereas mice in burn group (n = 7) received 15% TBSA full-thickness thermal injury, mice in burn + CORM-2 group (n = 7) underwent the same thermal injury with the immediate administration of CORM-2 (8 mg/kg intravenously), and mice in burn + DMSO group (n = 7) underwent the same thermal injury with an immediate 160 μl-bolus injection of 0.5% dimethyl sulfoxide/saline. Polymorphonuclear leucocyte (PMN) accumulation (assessed by the myeloperoxidase assay) was assessed in mice liver. Activation of nuclear factor kappa B (NF-&kgr;&Bgr;) and the expression levels of ICAM-1 and VCAM-1 in liver were assessed. In an in vitro experiment, sinusoidal endothelial cells (SECs) isolated from the liver of normal mice were stimulated by experimental mice serum (50% v/v) for 4 hours. Subsequently, the adhesion of PMNs to SECs was assessed. In addition, the number and states (rolling or stationary) of leukocytes in liver were observed by intravital microscopy. Treatment of thermally injured mice with CORM-2 attenuated PMN accumulation and prevented activation of NF-&kgr;&Bgr; in the liver, which was accompanied by a decrease of the expression of ICAM-1 and VCAM-1. In parallel, PMNs adhesion to SECs stimulated by CORM-2-treated thermally injured mice serum was markedly decreased. Intravital microscopy showed that the stationary leukocytes in thermally injured mice liver were significantly reduced by treatment of CORM-2. CORM-released CO attenuates leukocytes sequestration in the liver of burn mice by interfering with NF-&kgr;&Bgr; activation, protein expression of ICAM-1 and VCAM-1, and therefore suppressing endothelial cells proadhesive phenotype.
Demographic risk factors, mediators, and moderators in youths’ diabetes metabolic control

Background: Socioeconomic status (SES) is one of the most frequently identified and potent predictors of disease morbidity and mortality. It also predicts diabetes care and metabolic control, yet it is often confounded with parental marital status and ethnicity in pediatric samples.Purpose: Key demographic risk factors for poorer metabolic control in adolescents with type I diabetes are examined to distinguish their relative effects, along with disease care mediators and family environment moderators.Methods and Results: When SES, ethnicity, and marital status are considered simultaneously with path analysis, living with married biological parents is the sole predictor of better metabolic control in a predominantly middle-class sample. Specifically, adolescents who lived with their biologic parents had glycosylated hemoglobin levels that were approximately . 5% lower on average than those who lived in alternative family arrangements (i.e., blended and single-parent families). More frequent meals and snacks and more blood glucose monitoring mediates this effect. Under favorable conditions of greater familial harmony, children from married biologic families experience a stronger beneficial health effect, with average glycohemoglobin levels that are approximately . 81% lower in less conflicted families and . 62% lower in more cohesive families.Conclusions: In toto, marital status eclipsed the well known effects of SES in the prediction of metabolic control in a primarily middle-class sample of children with diabetes. The 8.0% average glycohemoglobin level of youths from married biologic families is similar to that of intensively treated adolescents in the Diabetes Control and Complications Trial and, if maintained, should be associated with clinically significant reductions in disease complications.