Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome optimization via virtual simulation to accelerate maize hybrid breeding

The employment of doubled-haploid (DH) technology in maize has vastly accelerated the efficiency of developing inbred lines. The selection of superior lines has to rely on genotypes with genomic selection (GS) model, rather than phenotypes due to the high expense of field phenotyping. In this work, we implemented 'genome optimization via virtual simulation (GOVS)' using the genotype and phenotype data of 1404 maize lines and their F1 progeny. GOVS simulates a virtual genome encompassing the most abundant 'optimal genotypes' or 'advantageous alleles' in a genetic pool. Such a virtually optimized genome, although can never be developed in reality, may help plot the optimal route to direct breeding decisions. GOVS assists in the selection of superior lines based on the genomic fragments that a line contributes to the simulated genome. The assumption is that the more fragments of optimal genotypes a line contributes to the assembly, the higher the likelihood of the line favored in the F1 phenotype, e.g. grain yield. Compared to traditional GS method, GOVS-assisted selection may avoid using an arbitrary threshold for the predicted F1 yield to assist selection. Additionally, the selected lines contributed complementary sets of advantageous alleles to the virtual genome. This feature facilitates plotting the optimal route for DH production, whereby the fewest lines and F1 combinations are needed to pyramid a maximum number of advantageous alleles in the new DH lines. In summary, incorporation of DH production, GS and genome optimization will ultimately improve genomically designed breeding in maize. Short abstract: Doubled-haploid (DH) technology has been widely applied in maize breeding industry, as it greatly shortens the period of developing homozygous inbred lines via bypassing several rounds of self-crossing. The current challenge is how to efficiently screen the large volume of inbred lines based on genotypes. We present the toolbox of genome optimization via virtual simulation (GOVS), which complements the traditional genomic selection model. GOVS simulates a virtual genome encompassing the most abundant 'optimal genotypes' in a breeding population, and then assists in selection of superior lines based on the genomic fragments that a line contributes to the simulated genome. Availability of GOVS (https://govs-pack.github.io/) to the public may ultimately facilitate genomically designed breeding in maize.
Advances in Nanotechnology-Based Biosensing of Immunoregulatory Cytokines

Cytokines are a large group of small proteins secreted by immune and non-immune cells in response to external stimuli. Much attention has been given to the application of cytokines’ detection in early disease diagnosis/monitoring and therapeutic response assessment. To date, a wide range of assays are available for cytokines detection. However, in specific applications, multiplexed or continuous measurements of cytokines with wearable biosensing devices are highly desirable. For such efforts, various nanomaterials have been extensively investigated due to their extraordinary properties, such as high surface area and controllable particle size and shape, which leads to their tunable optical emission, electrical, and magnetic properties. Different types of nanomaterials such as noble metal, metal oxide, and carbon nanoparticles have been explored for various biosensing applications. Advances in nanomaterial synthesis and device development have led to significant progress in pushing the limit of cytokine detection. This article reviews currently used methods for cytokines detection and new nanotechnology-based biosensors for ultrasensitive cytokine detection.
A network approach to posttraumatic stress disorder: Comparing interview and self-report networks.

OBJECTIVE Trauma-related fear (e.g., reexperiencing), impaired reward (e.g., anhedonia), and interpersonal (e.g., detachment) processes may be functionally intertwined, giving rise to chronic psychopathology after a trauma. Network analyses can help pinpoint symptom drivers and treatment targets, but studies examining posttraumatic stress disorder (PTSD) treatment-seeking individuals are lacking. METHOD Treatment-seeking adults with primary PTSD (N = 350) completed interview and self-report measures of PTSD severity (PSS-I; PSS-SR). Self-report and interview-based networks were estimated and compared. RESULTS Both networks suggested distinct but interconnected communities of reexperiencing and dysphoric symptoms (e.g., interpersonal detachment, numbing). Centrality profiles were strongly associated across networks (rs = .71), with cued reexperiencing and interpersonal detachment showing strong centrality. Self-reported symptoms were more interconnected, suggesting lower specificity. CONCLUSIONS For those seeking treatment, interrelated fear and interpersonal processes may drive functional impairment in PTSD, and interview-based networks may help better delineate influential symptoms. Therapeutically, targeting cued reexperiencing and interpersonal detachment may facilitate broader symptom decreases. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Risk Factors of Duodenobiliary Reflux-Related Dysfunction of Covered Biliary Metal Stents after Treatment of Duodenal Stricture in Patients with Malignant Biliary and Duodenal Obstruction

Abstract Duodenal obstruction is often accompanied with unresectable malignant distal biliary obstruction in patients who have undergone biliary self-expandable metal stent (SEMS) placement. Duodenobiliary reflux (DBR) is a major cause of recurrent biliary obstruction (RBO) after covered biliary SEMS placement. We analyzed the risk factors for DBR-related SEMS dysfunction following treatment for malignant duodenal obstruction. Sixty-one patients with covered SEMS who underwent treatment for duodenal obstruction were included. We excluded patients with tumor-related stent dysfunction (n = 6) or metal stent migration (n = 1). Fifty-four patients who underwent covered biliary SEMS placement followed by duodenal metal stenting or surgical gastrojejunostomy were included. Eleven patients had DBR-related biliary SEMS dysfunction after treatment of duodenal obstruction. There was no difference between the duodenal metal stenting group and the surgical gastrojejunostomy group. Duodenal obstruction below the papilla of Vater and a score of ≤2 on the Gastric Outlet Obstruction Scoring System after treatment for duodenal obstruction were associated with DBR-related covered biliary SEMS dysfunction. Thus, creating a reliable route for ensuring good oral intake and avoiding DBR in patients with duodenal obstruction below the papilla of Vater are both important factors in preventing DBR-related covered biliary SEMS dysfunction.
Broadband electro-optic polarization conversion with atomically thin black phosphorus

Description Metasurfaces tune polarization In photonic systems, the polarization state of light is typically manipulated with bulky components based on dielectrics and liquid crystals. Active metasurfaces now provide the possibility of shrinking the size of these components to the nanoscale. Biswas et al. demonstrate an active nanophotonic structure capable of versatile electro-optic polarization conversion. Using trilayer black phosphorus sandwiched between electrical gates forming a cavity, they show that the polarization state of light across telecommunication wavelengths can be electrically switched. Such control can be useful for a number of applications in communications, imaging, and beam steering where the wavefront of the propagating light can be actively manipulated. —ISO An active nanophotonic polarization convertor is demonstrated using trilayer black phosphorus. Active polarization control is highly desirable in photonic systems but has been limited mostly to discrete structures in bulky dielectric media and liquid crystal–based variable retarders. Here, we report electrically reconfigurable polarization conversion across telecommunication wavelengths (1410 to 1575 nanometers) in van der Waals layered materials using tri-layer black phosphorus (TLBP) integrated in a Fabry-Pérot cavity. The large electrical tunability of birefringence in TLBP enables spectrally broadband polarization control. We found that polarization states could be generated over a large fraction of the Poincaré sphere through spectral tuning, and that electrical tuning enables the state of polarization conversion to span nearly half the Poincaré sphere. We observed both linear to circular and cross-polarization conversion with voltage, demonstrating versatility with a high dynamic range.
Depth- and temperature-specific fatty acid adaptations in ctenophores from extreme habitats

ABSTRACT Animals are known to regulate the composition of their cell membranes to maintain key biophysical properties in response to changes in temperature. For deep-sea marine organisms, high hydrostatic pressure represents an additional, yet much more poorly understood, perturbant of cell membrane structure. Previous studies in fish and marine microbes have reported correlations with temperature and depth of membrane-fluidizing lipid components, such as polyunsaturated fatty acids. Because little has been done to isolate the separate effects of temperature and pressure on the lipid pool, it is still not understood whether these two environmental factors elicit independent or overlapping biochemical adaptive responses. Here, we use the taxonomic and habitat diversity of the phylum Ctenophora to test whether distinct low-temperature and high-pressure signatures can be detected in fatty acid profiles. We measured the fatty acid composition of 105 individual ctenophores, representing 21 species, from deep and shallow Arctic, temperate, and tropical sampling locales (sea surface temperature, −2° to 28°C). In tropical and temperate regions, remotely operated submersibles (ROVs) enabled sampling down to 4000 m. We found that among specimens with body temperatures 7.5°C or colder, depth predicted fatty acid unsaturation levels. In contrast, in the upper 200 m of the water column, temperature predicted fatty acid chain lengths. Taken together, our findings suggest that lipid metabolism may be specialized with respect to multiple physical variables in diverse marine environments. Largely distinct modes of adaptation to depth and cold imply that polar marine invertebrates may not find a ready refugium from climate change in the deep.
Self-Referenced Refractive Index Biosensing with Graphene Fano Resonance Modes

A hybrid structure composed of periodic monolayer graphene nanoribbons and a dielectric multilayer structure was designed to generate a Fano resonance (FR). The strong interaction between the surface plasmon resonance of graphene and the dielectric waveguide mode results in the FR. The finite element method is utilized to investigate the behaviors of the FR, and it matches well with the theoretical calculations using rigorous coupled wave theory. The results demonstrate that the profile of the FR can be passively tuned by the period of the graphene nanoribbons and actively tuned by the Fermi level of the graphene. The decoupled nature of the FR gives it potential applications as a self-calibrated refractive index biosensor, and the sensitivity can reach as high as 4.615 μm/RIU. Thus, this work provides a new idea for an excellent self-referencing refractive index biosensor.
Optimization of Membrane Protein TmrA Purification Procedure Guided by Analytical Ultracentrifugation

Membrane proteins are involved in various cellular processes. However, purification of membrane proteins has long been a challenging task, as membrane protein stability in detergent is the bottleneck for purification and subsequent analyses. Therefore, the optimization of detergent conditions is critical for the preparation of membrane proteins. Here, we utilize analytical ultracentrifugation (AUC) to examine the effects of different detergents (OG, Triton X-100, DDM), detergent concentrations, and detergent supplementation on the behavior of membrane protein TmrA. Our results suggest that DDM is more suitable for the purification of TmrA compared with OG and TritonX-100; a high concentration of DDM yields a more homogeneous protein aggregation state; supplementing TmrA purified with a low DDM concentration with DDM maintains the protein homogeneity and aggregation state, and may serve as a practical and cost-effective strategy for membrane protein purification.
Voltage-Gated Sodium Channels: A Prominent Target of Marine Toxins

Voltage-gated sodium channels (VGSCs) are considered to be one of the most important ion channels given their remarkable physiological role. VGSCs constitute a family of large transmembrane proteins that allow transmission, generation, and propagation of action potentials. This occurs by conducting Na+ ions through the membrane, supporting cell excitability and communication signals in various systems. As a result, a wide range of coordination and physiological functions, from locomotion to cognition, can be accomplished. Drugs that target and alter the molecular mechanism of VGSCs’ function have highly contributed to the discovery and perception of the function and the structure of this channel. Among those drugs are various marine toxins produced by harmful microorganisms or venomous animals. These toxins have played a key role in understanding the mode of action of VGSCs and in mapping their various allosteric binding sites. Furthermore, marine toxins appear to be an emerging source of therapeutic tools that can relieve pain or treat VGSC-related human channelopathies. Several studies documented the effect of marine toxins on VGSCs as well as their pharmaceutical applications, but none of them underlined the principal marine toxins and their effect on VGSCs. Therefore, this review aims to highlight the neurotoxins produced by marine animals such as pufferfish, shellfish, sea anemone, and cone snail that are active on VGSCs and discuss their pharmaceutical values.
Bariatric surgery on obese walking: mass(ive) changes akin to load carrying and hypogravity for normal‐weight adults

Obesity is a condition of adipose mass excess, associated with increased mortality and many health problems; given the high prevalence and health burden, it is critical to improve its prevention andmanagement. In a recent issue of The Journal of Physiology, Malatesta and colleagues (2022) investigated the impact of bariatric surgery and the subsequent large body mass loss on the energetics and mechanics of walking in obese participants, evaluated before and after surgery. Walking is themost common and practical means to promote physical activity and reduce sedentary behaviour. However, obese people have a higher absolute energy cost of walking – the energy above resting demands needed to walk for a unit distance (in J m−1) – than normal-weight people (for recent review see Peyré-Tartaruga et al. 2021). When energy cost is normalised to the unit of body mass (C; J kg−1 m−1), this difference persists, hinting that mass-independent factors are involved (e.g. gait pattern, muscle contractions at disadvantageous lengths or velocities; Malatesta et al. 2022). Such greater C leads obese people to increased effort during walking and favours sedentary behaviour. Knowing the causes of the greater C can bring insight into solutions that facilitate exercise in obese adults, leading to better health outcomes.
Musclin Is Related to Insulin Resistance and Body Composition, but Not to Body Mass Index or Cardiorespiratory Capacity in Adults

Background We studied whether musclin function in humans is related to glycemic control, body composition, and cardiorespiratory capacity. Methods A cross-sectional study was performed in sedentary adults with or without metabolic syndrome (MS). Serum musclin was measured by enzyme-linked immunosorbent assay. Insulin resistance (IR) was evaluated by the homeostatic model assessment (HOMA-IR). Body composition was determined by dual-energy X-ray absorptiometry and muscle composition by measuring carnosine in the thigh, a surrogate of fiber types, through proton magnetic resonance spectroscopy. Cardiorespiratory capacity was assessed through direct ergospirometry. Results The control (n=29) and MS (n=61) groups were comparable in age (51.5±6.5 years old vs. 50.7±6.1 years old), sex (72.4% vs. 70.5% women), total lean mass (58.5%±7.4% vs. 57.3%±6.8%), and peak oxygen consumption (VO2peak) (31.0±5.8 mL O2./kg.min vs. 29.2±6.3 mL O2/kg.min). Individuals with MS had higher body mass index (BMI) (30.6±4.0 kg/m2 vs. 27.4±3.6 kg/m2), HOMA-IR (3.5 [95% confidence interval, CI, 2.9 to 4.6] vs. 1.7 [95% CI, 1.1 to 2.0]), and musclin (206.7 pg/mL [95% CI, 122.7 to 387.8] vs. 111.1 pg/mL [95% CI, 63.2 to 218.5]) values than controls (P<0.05). Musclin showed a significant relationship with HOMA-IR (β=0.23; 95% CI, 0.12 to 0.33; P<0.01), but not with VO2peak, in multiple linear regression models adjusted for age, sex, fat mass, lean mass, and physical activity. Musclin was significantly associated with insulin, glycemia, visceral fat, and regional muscle mass, but not with BMI, VCO2peak, maximum heart rate, maximum time of work, or carnosine. Conclusion In humans, musclin positively correlates with insulinemia, IR, and a body composition profile with high visceral adiposity and lean mass, but low body fat percentage. Musclin is not related to BMI or cardiorespiratory capacity.
Effectiveness of Mindfulness-Based Relapse Prevention in Individuals with Substance Use Disorders: A Systematic Review

Objectives: This systematic review aimed to understand the current state of the art about the effectiveness of mindfulness-based relapse prevention (MBRP) on individuals with substance use disorders (SUD), taking into account not only SUD variables (e.g., cravings, frequency of use) but also other relevant clinical variables (e.g., anxiety and depressive symptoms, quality of life). Methods: A comprehensive search of electronic databases was conducted to identify studies that investigate MBRP interventions on individuals with SUD. Studies that met the inclusion criteria were synthesized and assessed using systematic review methods. Results: Thirteen studies were included in the present review. The methodological quality of the included studies was moderately strong. Nine studies (69.2%) used the traditional 16 h MBRP program. Six studies (46.1%) chose to use a co-intervention treatment ranging from the treatment as usual (TAU) to cognitive behavioral therapy. All but one study indicated that their interventions produced positive effects on at least one addiction outcome measure. None of the interventions were evaluated across different settings or populations. Conclusions: Despite some heterogeneity regarding the type of MBRP program used, results support the effectiveness of these interventions in the SUD population, especially in reducing cravings, decreasing the frequency of use, and improving depressive symptoms.
Self-Management Education Class Attendance and Health Care Provider Counseling for Physical Activity Among Adults with Arthritis — United States, 2019

Arthritis is a highly prevalent and disabling condition among U.S. adults (1); arthritis-attributable functional limitations and severe joint pain affect many aspects of health and quality of life (2). Self-management education (self-management) and physical activity can reduce pain and improve the health status and quality of life of adults with arthritis; however, in 2014, only 11.4% and 61.0% of arthritis patients reported engaging in each, respectively. To assess self-reported self-management class attendance and health care provider physical activity counseling among adults with doctor-diagnosed arthritis, CDC analyzed 2019 Behavioral Risk Factor Surveillance System (BRFSS) data. In 2019, an age-standardized state median of one in six (16.2%) adults with arthritis reported ever attending a self-management class, and 69.3% reported ever receiving health care provider counselling to be physically active. Prevalences of both differed by state and sociodemographic characteristics; decreased with lower educational attainment, joint pain severity, and urbanicity; and were lower in men than in women. Health care providers can play an important role in promoting self-management class attendance and physical activity by counseling arthritis patients about their benefits and referring patients to evidence-based programs (3).
New Advances in Tissue Metabolomics: A Review

Metabolomics offers a hypothesis-generating approach for biomarker discovery in clinical medicine while also providing better understanding of the underlying mechanisms of chronic diseases. Clinical metabolomic studies largely rely on human biofluids (e.g., plasma, urine) as a more convenient specimen type for investigation. However, biofluids are non-organ specific reflecting complex biochemical processes throughout the body, which may complicate biochemical interpretations. For these reasons, tissue metabolomic studies enable deeper insights into aberrant metabolism occurring at the direct site of disease pathogenesis. This review highlights new advances in metabolomics for ex vivo analysis, as well as in situ imaging of tissue specimens, including diverse tissue types from animal models and human participants. Moreover, we discuss key pre-analytical and post-analytical challenges in tissue metabolomics for robust biomarker discovery with a focus on new methodological advances introduced over the past six years, including innovative clinical applications for improved screening, diagnostic testing, and therapeutic interventions for cancer.
One tie to capture advice and friendship: Leader multiplex centrality effects on team performance change.

Because leaders' authority is often insufficient to change team performance, formal team leaders seek informal influence through the occupation of central positions in social networks. Prior research focuses on leader centrality involving simplex ties, that is, either friendship or advice, to the neglect of multiplex ties that involve the overlap of friendship and advice. Friendship and advice ties offer different but complementary resources, so leader centrality in one but not the other network limits leader influence. We provide theory and evidence concerning how leader multiplex centrality affects team performance improvement, particularly if leaders are embedded in team social contexts with sparse friendship and numerous adversarial ties. The research context involved 84 ongoing public university service teams headed by formal leaders. Our results show the importance of leader multiplex centrality relative to leader simplex centrality. First, leader multiplex centrality predicted team performance change over a 2-year period more strongly than leader centrality in either the advice or the friendship team network. Second, leader multiplex centrality positively predicted team performance change for teams featuring dense adversarial networks or sparse friendship networks. It is not sufficient, therefore, for leaders to be either liked or regarded as expert. It is the integration of both advice and friendship in one tie between the leader and followers that facilitates performance change. (PsycInfo Database Record (c) 2021 APA, all rights reserved).