Miracle-dz/UniFAR-FTUs huggingface dataset:
Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance

Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in functions involved in genome integrity. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent than that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that environmentally transmitted symbionts that associate with individual hosts over their lifetime show features of narrow symbioses, where the frequency of HGT is constrained.
Effect of Robot-Assisted Training on EEG-Derived Movement-Related Cortical Potentials for Post-Stroke Rehabilitation–A Case Series Study

This paper deploys movement-related cortical potential (MRCP), an electroencephalogram (EEG)-derived time-domain pattern, to assess the effect of robot-assisted motor training in seven post-stroke patients with hand impairment. Patients are divided into two groups of four subjects with supratentorial lesions and a group of three subjects with infratentorial lesions. Both groups participate in multiple-session motor training for their affected hand with an AMADEO rehabilitation robot. During pre- and post-training periods, three assessment procedures which include EEG signals derived from eight specific electrodes, hand-kinematic parameters, and clinical tests are performed. After four weeks of training, the negative peak of the MRCP signals shows a decrease across all electrodes and reaches significance in seven out of the eight electrodes for the first group according to paired t-test ( $p < 0.05$ ). Whereas for the second group, the MRCP signal shows a decrease in its negative peak across all electrodes and reaches significance in two of the eight electrodes (paired t-test, $p < 0.05$ ) after eight weeks. Moreover, these MRCP changes show a positive association with improvements in kinematic parameters and clinical test results for both groups. Hence, this study shows that improvement of clinical outcomes in robot-assisted training is associated with a reduction in the amplitude of the MRCP signal. Furthermore, infratentorial stroke patients show a slower clinical improvement and require longer rehabilitation to produce significant changes in MRCP compared to subjects with supratentorial stroke.
Circulating Extracellular Vesicles Contain Liver-Derived RNA Species as Indicators of Severe Cholestasis-Induced Early Liver Fibrosis in Mice

Aims: Biliary diseases represent around 10% of all chronic liver diseases and affect both adults and children. Currently available biochemical tests detect cholestasis but not early liver fibrosis. Circulating extracellular vesicles (EVs) provide a noninvasive, real-time molecular snapshot of the injured organ. We thus aimed at searching for a panel of EV-based biomarkers for cholestasis-induced early liver fibrosis using mouse models. Results: Progressive and detectable histological evidence of collagen deposition and liver fibrosis was observed from day 8 after bile duct ligation (BDL) in mice. Whole transcriptome and small RNA sequencing analyses of circulating EVs revealed differentially enriched RNA species after BDL versus sham controls. Unsupervised hierarchical clustering identified a signature that allowed for discrimination between BDL and controls. In particular, 151 microRNAs (miRNAs) enriched in BDL-derived EVs were identified, of which 66 were conserved in humans. The liver was an important source of circulating EVs in BDL animals as evidenced by the enrichment of several hepatic mRNAs, such as Albumin and Haptoglobin. Interestingly, among experimentally validated miRNAs, miR192-5p, miR194-5p, miR22-3p, and miR29a-3p showed similar enrichment patterns also in EVs derived from 3,5-diethoxycarboncyl-1,4-dihydrocollidine-treated (drug-induced severe cholestasis) but not in mice with mild phenotype or non-cholestatic liver fibrosis. Innovation: A panel of mRNAs and miRNAs contained in circulating EVs, when combined, indicates hepatic damage and fibrosis in mice and represents promising biomarkers for human severe cholestasis-induced liver fibrosis. Conclusion: Analysis of EV-based miRNAs, in combination with hepatic injury RNA markers, can detect early cholestatic liver injury and fibrosis in mice. Antioxid. Redox Signal. 36, 480–504.
Carsharing Demand Estimation

Worldwide carsharing has grown significantly in recent years. The traditional round-trip model is no longer the only carsharing model offered. It is now being accompanied by more flexible options such as one-way station-based, free-floating and peer-to-peer carsharing. Moreover, it has become important to have tools that can estimate both the spatial and temporal demand for carsharing services, providing operators with a good instrument for planning their services. The work presented in this paper makes use of the multiagent simulation tool (MATSIM) to investigate the effects of supply on the demand of the existing round-trip service in the Zurich area of Switzerland. Additionally, the results provide guidance for the possible optimization of the carsharing service. Also presented is an implementation of a one-way station-based model as a part of the MATSIM framework as well as an investigation of the potentials of one-way carsharing service in the study area. Results show that there is still untapped potential of round-trip carsharing, but that service might need optimization. Furthermore, because of greater convenience, one-way carsharing would generate slightly less than three times more trips compared with the round-trip option.
Computationally Attractive and Location Robust Estimator for IoT Device Positioning

Locating a device is a basic element for many Internet of Things (IoT) applications. In particular, it often demands an algorithm having low complexity to limit the energy consumption and most important, sufficient robustness without knowing the device in the near-field for point localization or in the far-field for direction of arrival (DOA) estimation. This article proposes a new localization algorithm that can achieve the two purposes, with the theoretical analysis to validate the optimal accuracy and the real data experiment to support the promising performance. The first objective is achieved by a closed-form solution and the second is accomplished by using the modified polar representation (MPR) of the source position, based on a new formulation for the localization problem. While the MPR localization method has been introduced before, it is not sufficiently robust for IoT application to handle the large equal radius (LER) scenario or the presence of sensor position errors. The proposed algorithm uses a different MPR formulation, which is able to handle the LER scenario, sensor position errors, and has low computational complexity.
Understanding the Picturesque nature of the Lower St. Croix National Scenic and Recreational Riverway: The integrated use of historical and survey research and geographic information systems technology

Aesthetic expectations of Americans visiting the Lower St Croix National Scenic and Recreational Riverway (riverway), a unit of the United States National Park System stretching along an 84 kilometre reach of the St Croix River between Minnesota and Wisconsin, are rooted in eighteenth-century Picturesque Theory. The ability to decode and map the landscape dimensions of picturesque value makes it possible to manage better visitor expectations related to the picturesque ideal. This paper translates picturesque values distilled from analysis of eighteenth-century theoretical literature, literary accounts of nineteenth-century visitors to the riverway and twentieth-century perceptions of riverway stakeholders into mappable landscape dimensions, which are used to create a spatial model of picturesque value with geographic information systems (GIS) technology.
Comparing Genetic Variation among Latin American Immigrants: Implications for Forensic Casework in the Arizona- and Texas-Mexico Borderlands

ABSTRACT The humanitarian crisis on the US-Mexico border is a long-standing and evolving crisis in which nearly 8,000 deaths have been reported in the last two decades. These deaths are largely distributed across the Arizona-Mexico and Texas-Mexico border regions, where demographic trends for immigrants attempting to cross into the United States have shifted dramatically. The demographic change and volume of immigrants seeking shelter in the United States present new challenges for the forensic practitioners entrusted with the identification of individuals who lose their lives during the final segment of their journey. Within this border context, this study investigated how genetic variation inferred from forensically significant microsatellites can provide valuable information on regions of origin for unidentified remains at the group level. To explore how to mobilize these genetic data to inform identification strategies, the authors conducted a comparative genetic analysis of identified and unidentified immigrant cases from the Arizona- and Texas-Mexico contexts, as well as 27 other Latin American groups. Allele frequencies were utilized to calculate FST, and relationships were visually depicted in a multidimensional scaling plot. A Spearman correlation coefficient analysis assessed the strength and significance of population relationships, and an agglomerative clustering analysis assessed population clusters. Results indicate that Arizona-Mexico immigrants have the strongest relationship (>80%) with groups from El Salvador, Guatemala, Mexico, and an indigenous group from southern Mexico. Texas-Mexico immigrants have the strongest relationships (>80%) with groups from Belize, Colombia, Costa Rica, El Salvador, Guatemala, Honduras, and Nicaragua. These findings agree with, and are discussed in comparison with, previously reported demographic trends, population genetics research, and population history analyses. The authors emphasize the utility and necessity of coupling genetic variation research with a nuanced anthropological perspective for identification processes in the US-Mexico border context.
“We Support You … to an Extent”: Identities, Intersections, and Family Support Among First-Generation Students in a School of Social Work

Family support is a critical part of college student retention. Given the strength of parental educational attainment in predicting access and persistence among college students (Choy, 2001), some have questioned the capacity for families to support first-generation college students. Family support may be especially critical for first-generation college students, who value interdependence more highly than continuing generation students (Stephens et al., 2012). This paper centers the perspectives of first-generation students in a school of social work and their experiences of family support. Focus group conversations were analyzed using the Listening Guide/Voice-centered relational data analysis (Brown & Gilligan, 1992). My interpretations were also guided by Black Feminist Thought (Crenshaw, 2000; Hill Collins, 1990) and Post-Modern Feminism (Campbell & Wasco, 2000), offering an intersectional, relationally-focused analysis of the nuances of family support. Findings highlight students’ perceptions of family support, and the role that cultural expectations related to gender, race, and class play in shaping contradictory messages of family support. I offer implications for educators in schools of social work, including troubling narratives of social mobility, as part of the larger project of enhancing social justice in academia (Saulnier & Swigonski, 2006).
Analyses of advanced concepts in multi-stage gyro-amplifiers and startup in high-power gyro-oscillators

Title of Document: ANALYSES OF ADVANCED CONCEPTS IN MULTI-STAGE GYRO-AMPLIFIERS AND STARTUP IN HIGH POWER GYROOSCILLATORS. Oleksandr V. Sinitsyn, Doctor of Philosophy, 2005 Directed By: Professor V. L. Granatstein, Department of Electrical and Computer Engineering Gyrotrons are well recognized sources of high-power coherent electromagnetic radiation. The power that gyrotrons can radiate in the millimeterand submillimeter-wavelength regions exceeds the power of classical microwave tubes by many orders of magnitude. In this work, the author considers some problems related to the operation of gyro-devices and methods of their solution. In particular, the selfexcitation conditions for parasitic backward waves and effect of distributed losses on the small-signal gain of gyro-TWTs are analyzed. The corresponding small-signal theory describing two-stage gyro-traveling-wave tubes (gyro-TWTs) with the first stage having distributed losses is presented. The theory is illustrated by using it for the description of operation of a Ka-band gyro-TWT designed at the Naval Research Laboratory. Also, the results of nonlinear studies of this tube are presented and compared with the ones obtained by the use of MAGY, a multi-frequency, selfconsistent code developed at the University of Maryland. An attempt to build a large signal theory of gyro-TWTs with tapered geometry and magnetic field profile is made and first results are obtained for a 250 GHz gyro-TWT. A comparative small-signal analysis of conventional four-cavity and threestage clustered-cavity gyroklystrons is performed. The corresponding point-gap models for these devices are presented. The efficiency, gain, bandwidth and gainbandwidth product are analyzed for each scheme. Advantages of the clustered-cavity over the conventional design are discussed. The startup scenarios in high-power gyrotrons and the most important physical effects associated with them are considered. The work presents the results of startup simulations for a 140 GHz, MW-class gyrotron developed by Communications and Power Industries (CPI) for electron-cyclotron resonance heating (ECRH) and current drive experiments on the “Wendelstein 7-X” stellarator plasma. Also presented are the results for a 110 GHz, 1.5 MW gyrotron currently being developed at CPI. The simulations are carried out for six competing modes and with the effects of electron velocity spread and voltage depression taken into account. Also, the slow stage of the startup in long-pulse gyrotrons is analyzed and attention is paid to the effects of ion compensation of the beam space charge, frequency deviation due to the cavity wall heating and beam current decrease due to cathode cooling. These effects are modeled with a simple nonlinear theory and the code MAGY. ANALYSES OF ADVANCED CONCEPTS IN MULTI-STAGE GYROAMPLIFIERS AND STARTUP IN HIGH POWER GYRO-OSCILLATORS.
Spectral Analysis of Individual Terrestrial Gamma‐Ray Flashes Detected by ASIM

The Atmosphere‐Space Interactions Monitor (ASIM) is the first instrument in space specifically designed to observe terrestrial gamma‐ray flashes (TGFs). TGFs are high energy photons associated with lightning flashes and we perform the spectral analysis of 17 TGFs detected by ASIM. The TGF sample is carefully selected by rigorous selection criteria to keep a clean sample suitable for spectral analysis, that is, suitable count statistics, low instrumental effects, and reliable source location. Monte Carlo modeling of individual TGFs has been compared to the observed energy spectra to study the possible source altitudes and beaming geometries. A careful model of the instrumental effects has been developed and validated. Several combinations of source altitudes and beaming geometries are accepted by the statistical tests for all the TGFs in the sample resulting in a large uncertainty in the estimate of the intrinsic source luminosity. The analyzed TGFs show significant variations in observed fluence independent of the distance between source and ASIM. A lower limit on the maximum photon energy produced by TGFs is estimated to be 24 MeV for the analyzed TGFs. The intrinsic limitations of TGF spectral analysis from space are also investigated and it is found that the ability to constrain the source altitude and beaming geometries of TGFs strongly depends on the distance between source and satellite. With the current generation of instruments with effective areas in the range of few hundreds cm2, it is very difficult to constrain reliably the source properties without the help of simultaneous measurements in the radio band.
Electrical stimulated GLUT4 signalling attenuates critical illness‐associated muscle wasting

Critical illness myopathy (CIM) is a debilitating condition characterized by the preferential loss of the motor protein myosin. CIM is a by‐product of critical care, attributed to impaired recovery, long‐term complications, and mortality. CIM pathophysiology is complex, heterogeneous and remains incompletely understood; however, loss of mechanical stimuli contributes to critical illness‐associated muscle atrophy and weakness. Passive mechanical loading and electrical stimulation (ES) therapies augment muscle mass and function. While having beneficial outcomes, the mechanistic underpinning of these therapies is less known. Therefore, here we aimed to assess the mechanism by which chronic supramaximal ES ameliorates CIM in a unique experimental rat model of critical care.
STUDY ON MARKETING PATTERN OF APPLE CULTIVATION IN KASHMIR VALLEY, INDIA

An attempt has been made in this paper to evaluate the price spread of apple in the state of Jammu and Kashmir; the study is confined to Baramulla and Pulwama district with 35 growers, who were selected randomly from six selected villages considered to collect the required information. The primary data were collected from the apple growers through personal interview method with the help of well prepared pre tested schedule for the year 2019-20. For the present study 4 marketing channel were identified for the transaction of apple i.e.; Producer - Aratiya - Wholesale - Retailer - Consumer; Producer - Pre-harvest Contractor - Wholesaler - Retailer - Consumer, Producer - Post-harvest - Contractor -Wholesaler - Retailer - Consumer and Producer - Commission Agent - Wholesaler – Retailer - Consumer. Thus it can be concluded that the apple business in Kashmir is more remunerative. This enterprise is not only profitable and financially viable but also provides employment to large number of people in the valley area. The area and production of the apple is increasing at the fast rate, but the various defects of the existing marketing system results in the least share to the producer. Net return from the apple business can further be increased if the problems and defects of existing marketing system as stated above are taken care of. It can also be concluded that apple growing is more beneficial on all producers.
Deep vein thrombosis and our treatment applications: 12-year results

Introduction: Deep vein thrombosis is an important health problem that is frequently encountered in the general population and especially in surgical clinics and has a negative impact on quality of life. In this study, treatment options and results of patients with deep vein thrombosis who have been hospitalized for 12 years in Atatürk University and Erzurum Regional Hospital were examined and discussed. Methods: In our clinic, 412 cases of deep vein thrombosis (211 female, 201 male) were hospitalized between 2009 and 2021. The mean age of the patients was 49 ± 19 years. While medical treatment with heparin was given to all 412 patients; thrombolytic therapy, surgical embolectomy (vascular and pulmoner), and pharmaco-mechanical thrombectomy were applied to some of these patients. Results: Deep vein thrombosis was more common in the lower extremity (n=322, 78.2%). All patients had at least one of the complaints of pain, swelling and redness. All cases were diagnosed by color Doppler ultrasonography. Medically, standard and low molecular weight heparin therapy was given to all patients after hospitalization. Thrombolytic therapy was applied to 66 (16,1%) of the cases, pulmonary embolectomy to 8 (1,9%), surgical thrombectomy to 10 (2,4%) and pharmacomechanical thrombectomy to 44 (10,7%) patients. In addition to these 120 patients (29.1%), a vena cava filter was placed for prophylactic purposes. Conclusions: In patients diagnosed with deep vein thrombosis and hospitalized, the diagnosis should be supported by Doppler ultrasound in addition to clinical diagnosis after an etiology investigation. Early diagnosis, rapid and effective treatment methods are important for the subsequent quality of life of patients. In addition to low molecular weight heparins being the first choice agents, standard heparin administration still needs to be applied in some clinical pictures. In addition, we believe that pharmacomechanical thrombectomy can be applied in appropriate acute cases. Keywords: Deep vein thrombosis; anticoagulant treatment; heparin therapy; low-molecular-weight heparin; mechanical thrombectomy.
Fatality Risk for Motorcyclists in Fixed Object Collisions

Motorcyclists contribute significantly to road trauma around the world through the high incidence of serious injuries and fatalities. Around one fourth of motorcyclist fatalities may be attributed to collisions with fixed objects. A greater understanding of factors associated with fatalities occurring from fixed object collisions will enable safer roadway infrastructure design for motorcyclists. In this article, a multiple variable logistic regression model is developed to determine such factors, from a nationally representative weighted sample of around 30,000 single-vehicle fixed object motorcycle collisions which occurred in the United States over the 10-year period between 2000 and 2009. Additionally, a single variable logistic regression model is developed for motorcyclist fatality risk from fixed object collisions as a function of travel speed. This model may be a useful predictive tool for implementing motorcyclist safety strategies.