Miracle-dz/UniFAR-FTUs huggingface dataset:
A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome

Cladosporium fulvum is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of C. fulvum. The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of C. fulvum, indicating that Chr14 is dispensable. Thus, C. fulvum is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of C. fulvum Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the C. fulvum Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in C. fulvum Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the ‘two-speed genome’ model of evolution. Overall, the new reference genome of C. fulvum presents several notable features and is a valuable resource for studies in plant pathogens.
Blended Treatment for Alcohol Use Disorder (Blend-A): Explorative Mixed Methods Pilot and Feasibility Study

Background In Denmark, approximately 150,000 people have alcohol use disorder (AUD). However, only approximately 10% seek AUD treatment, preferably outside conventional health care settings and opening hours. The AUD treatment area experiences low adherence to treatment, as well as high numbers of no-show and premature dropouts. Objective The purpose of the Blend-A (Blended Treatment for Alcohol Use Disorder) feasibility and pilot study was to describe the process of translating and adapting the Dutch treatment protocol into Danish and Danish culture with a high amount of user involvement and to report how patients and therapists perceived the adapted version, when trying it out. Methods The settings were 3 Danish public municipal outpatient alcohol clinics. Study participants were patients and therapists from the 3 settings. Data consisted of survey data from the System Usability Scale, individual patient interviews, and therapist group interviews. Statistical analyses were conducted using the Stata software and Excel. Qualitative analysis was conducted using a theoretical thematic analysis. Results The usability of the treatment platform was rated above average. The patients chose to use the blended treatment format because it ensured anonymity and had a flexible design. Platform use formed the basis of face-to-face sessions. The use of the self-determined platform resulted in a more thorough process. Patient involvement qualified development of a feasible system. Managerial support for time use was essential. Guidance from an experienced peer was useful. Conclusions This study indicates that, during the processes of translating, adapting, and implementing blended, guided, internet-based, and face-to-face AUD treatment, it is relevant to focus on patient involvement, managerial support, and guidance from experienced peers. Owing to the discrete and flexible design of the blended offer, it appears that it may reach patient groups who would not otherwise have sought treatment. Therefore, blended treatment may increase access to treatment and contribute to reaching people affected by excessive alcohol use, who would not otherwise have sought treatment. In addition, it seems that the blended offer may enhance the participants’ perceived satisfaction and the effect of the treatment course. Thus, it appears that Blend-A may be able to contribute to existing treatment offers. Such findings highlight the need to determine the actual effect of the Blend-A offer; therefore, an effectiveness study with a controlled design is warranted.
Auxilin is a novel susceptibility gene for congenital heart block which directly impacts fetal heart function

Objective Neonatal lupus erythematosus (NLE) may develop after transplacental transfer of maternal autoantibodies with cardiac manifestations (congenital heart block, CHB) including atrioventricular block, atrial and ventricular arrhythmias, and cardiomyopathies. The association with anti-Ro/SSA antibodies is well established, but a recurrence rate of only 12%–16% despite persisting maternal autoantibodies suggests that additional factors are required for CHB development. Here, we identify fetal genetic variants conferring risk of CHB and elucidate their effects on cardiac function. Methods A genome-wide association study was performed in families with at least one case of CHB. Gene expression was analysed by microarrays, RNA sequencing and PCR and protein expression by western blot, immunohistochemistry, immunofluorescence and flow cytometry. Calcium regulation and connectivity were analysed in primary cardiomyocytes and cells induced from pleuripotent stem cells. Fetal heart performance was analysed by Doppler/echocardiography. Results We identified DNAJC6 as a novel fetal susceptibility gene, with decreased cardiac expression of DNAJC6 associated with the disease risk genotype. We further demonstrate that fetal cardiomyocytes deficient in auxilin, the protein encoded by DNAJC6, have abnormal connectivity and Ca2+ homoeostasis in culture, as well as decreased cell surface expression of the Cav1.3 calcium channel. Doppler echocardiography of auxilin-deficient fetal mice revealed cardiac NLE abnormalities in utero, including abnormal heart rhythm with atrial and ventricular ectopias, as well as a prolonged atrioventricular time intervals. Conclusions Our study identifies auxilin as the first genetic susceptibility factor in NLE modulating cardiac function, opening new avenues for the development of screening and therapeutic strategies in CHB.
Adoptive tumor infiltrating lymphocytes cell therapy for cervical cancer

ABSTRACT Cervical cancer is one of the most common malignancies among females. As a virus-related cancer, cervical cancer has attracted a lot of attention to develop virus-targeted immune therapy, including vaccine and adoptive immune cell therapy (ACT). Adoptive tumor infiltrating lymphocytes (TILs) cell therapy has been found to be able to control advanced disease progression in some cervical cancer patients who have received several lines of treatment in a pilot clinical trial. In addition, sustainable therapeutic effect has been identified in some cases. The safety risks of TIL therapy for patients are minimal or at least manageable. In this review, we focused on the versatility of TILs and tried to summarize potential strategies to improve the therapeutic effect of TILs and discuss related perspectives.
Hematology/Oncology Fellowship Programs' Participation in the Quality Oncology Practice Initiative

PURPOSE: In the first decade of this millennium, ASCO pioneered a quality measurement tool, the Quality Oncology Practice Initiative (QOPI). Despite an Accreditation Council for Graduate Medical Education (ACGME) requirement since 2012 for oncology fellows to participate in quality improvement (QI) projects, the uptake of QOPI remains modest. METHODS: This study examined reasons for low QOPI participation by surveying participating and nonparticipating HemOnc Fellowship Programs. The survey elicited views toward QI and QOPI as well as ideas about making the program more helpful. RESULTS: Among 69 fellowship programs, only 39% (n = 27) participated in QOPI. Other findings were that (1) the majority of programs considered their fellows' QI projects beneficial but were not fulfilling the ACGME standard for all fellows' QI participation; (2) nonparticipating programs were unfamiliar with but interested in QOPI; (3) participating programs tended to view QI as easier to conduct and more beneficial than nonparticipating programs; and (4) programs that withdrew from QOPI and participating programs alike were dissatisfied with the educational benefit and data abstraction burden for fellows. CONCLUSION: Academic oncology programs generally valued QI but many have not fully engaged in it. Fellows in programs participating in QOPI may have had less difficulty conducting QI and their projects may have been more beneficial than that of nonparticipating programs. However, perceived lack of educational benefits for fellows and the burden of manual data abstraction from the electronic medical record are impediments to satisfaction with the program. Higher faculty involvement and longitudinal reports for each fellow may significantly increase participation. Review of Hem/Onc Fellowship Programs' participation in the ASCO Quality Oncology Practice Initiative.
Overweight and Obese Status Is Not Associated With Disease Activity for Children and Adolescents With Newly Diagnosed Inflammatory Bowel Disease

INTRODUCTION: Despite the high prevalence of pediatric obesity, its impact on Crohn's disease (CD) and ulcerative colitis (UC) activity remains poorly characterized. The aim of this study was to evaluate disease-related outcomes in overweight and obese children with CD and UC. METHODS: We conducted a retrospective cohort study using the ImproveCareNow Network, a multicenter registry of children with inflammatory bowel disease. We included children with newly diagnosed CD and UC enrolled in ImproveCareNow Network from September 2006 to December 2018 who had at least 1 follow-up visit 12–18 months after diagnosis. Patients were stratified into normal weight, overweight, or obese categories. Primary outcome was remission at 1 year based on physician's global assessment (PGA); key secondary outcomes included short pediatric CD activity index and pediatric UC activity index. RESULTS: There were 4,972 children included (70% CD). Compared with normal weight, obese and overweight children with CD did not have worse disease activity at 1 year based on PGA. However, obese children did have modestly worse disease activity based on short pediatric CD activity index (inactive 43% vs 58%, mild 48% vs 36%, and moderate-severe 9% vs 7% for obese vs normal weight, P < 0.01). For children with UC, there were no differences in disease activity at 1 year based on PGA or pediatric UC activity index. Logistic regression mirrored these findings. DISCUSSION: Obese and overweight children with newly diagnosed inflammatory bowel disease do not seem to have worsened disease activity at 1 year after diagnosis compared with normal weight children.
Improving the Culture of Safety: A Prospective Handoff Initiative from the Operating Room to the Trauma Intensive Care Unit

A recent EAST publication emphasized the importance of handoffs to ensure safe and effective care for trauma patients. In this work, we evaluated our existing handoffs from the operating room (OR) to the trauma intensive care unit (TICU) and implemented a formal process at our level 1 trauma center. Pre and post-intervention surveys were offered to the stakeholders. Responses were recorded in a Likert scaled format and results were compared using Student’s t-test with statistical significance was set to . 05. 57 surveys were completed (30 pre, 27 post) and 139 handoffs occurred. There was significant improvement in “overall satisfaction” and “understanding of information expected. ” Standardizing an OR to intensive care unit handoff clarifies expectations and improves care team satisfaction. While future studies are needed to evaluate the impact of structured handoffs on patient outcomes, provider satisfaction likely serves as an indicator for culture shift towards safer transitions of care for injured patients.
Pragmatic Uncontrolled Study of Specialized Cognitive Behavioral Therapy for Adults With Chronic Tinnitus

Objectives: Tinnitus is the perception of sound without an external source, affecting quality of life that can cause severe distress in approximately 1 to 3% of the population of people with tinnitus. Randomized controlled trials of cognitive behavioral therapy for tinnitus have demonstrated its effectiveness in improving quality of life, but the effects of their implementation on a large scale in routine practice remains unknown. Therefore, the main purpose of this study was to examine the effects of stepped-care cognitive behavioral therapy for tinnitus delivered in a tertiary audiological center of a regional hospital. Second, we wished to examine predictors of favorable outcome. Design: Four hundred three adults with chronic tinnitus were enrolled in this prospective observational study (at 3 months, N=334, 8 months, N=261; 12 months, N=214). The primary outcome was health-related quality of life as measured by the Health Utilities Index III (HUI-III) at 12 months. Secondary outcomes were self-reported levels of tinnitus-related distress, disability, affective distress and tinnitus-related negative beliefs and fear. Measures were completed pre-intervention at 3 months, 8 months, and 12 months. Multilevel modeling was used to examine effects and their predictors. Results: Younger participants with lower levels of tinnitus distress were more likely to dropout while those with higher tinnitus distress at baseline and quality of life were more likely to receive step 2 of treatment. MLM analyses revealed, with one exception, no relation between any baseline variable and outcome change over time. Most participants’ improvement exceeded minimally clinical important difference criteria for quality of life, tinnitus-related handicap, and tinnitus distress. Conclusions: Results from this large pragmatic study complements those from randomized controlled trials of cognitive behavioral therapy for chronic tinnitus distress and supports its implementation under “real-world” conditions.
Predicting physical activity in kidney transplant recipients: an application of the Health Action Process Approach model

ABSTRACT Despite numerous physical, psychological, and social benefits of physical activity (PA), few kidney transplant recipients (KTRs) positively participate in PA. It is essential to understand the influencing factors of PA in KTRs. This study aimed to apply the Health Action Process Approach (HAPA) model to explore the influencing factors of PA in KTRs. This was a prospective study involving 320 participants. Pre-actional self-efficacy, outcome expectancies, risk perception, social support, PA intention, and demographic and clinical data were measured at Time 1. Coping self-efficacy, planning, recovery self-efficacy, and PA behavior were assessed 3 months later. The hypothesized relationships were examined by structural equation modeling. Findings revealed significant direct effects of pre-actional self-efficacy, negative outcome expectancies, positive outcome expectancies, and social support on intention. Planning and recovery self-efficacy were significant predictors of PA. The HAPA model provided a validated and useful framework for predicting the factors influencing PA behavior in KTRs.
Computerized Cognitive Behavioral Therapy Intervention for Depression Among Veterans: Acceptability and Feasibility Study

Background Computerized cognitive behavioral therapies (cCBTs) have been developed to deliver efficient, evidence-based treatment for depression and other mental health conditions. Beating the Blues (BtB) is one of the most empirically supported cCBTs for depression. The previous trial of BtB with veterans included regular guidance by health care personnel, which increased the complexity and cost of the intervention. Objective This study, conducted by researchers at a Veterans Affairs Medical Center, aims to test the acceptability and feasibility of unguided cCBT for depression among US military veterans. Methods To examine the acceptability of BtB delivered without additional peer or other mental health care provider support, a before-and-after trial was conducted among United States (US) military veterans experiencing mild to moderate depressive symptoms. The feasibility of the study design for a future efficacy trial was also evaluated. Results In total, 49 veterans completed preintervention assessments and received access to BtB, and 29 participants completed all postintervention assessments. The predetermined acceptability criterion for the intervention was met. Although the predetermined feasibility criteria regarding screening eligibility rate, number of BtB modules completed, and completion of a posttreatment assessment were not met, the results were comparable with those of other cCBT studies. Conclusions This is the first study among US military veterans to demonstrate support for the implementation of cCBT for depression without the assistance of a mental health professional or a peer support specialist, suggesting that stand-alone computer-aided interventions may be viable. Ideas for improving feasibility in future trials based on this study are discussed.
The role of motor proteins in photoreceptor protein transport and visual function

ABSTRACT Background Rods and cones are photoreceptor neurons in the retina that are required for visual sensation in vertebrates, wherein the perception of vision is initiated when these neurons respond to photons in the light stimuli. The photoreceptor cell is structurally studied as outer segments (OS) and inner segments (IS) where proper protein sorting, localization, and compartmentalization are critical for phototransduction, visual function, and survival. In human retinal diseases, improper protein transport to the OS or mislocalization of proteins to the IS and other cellular compartments could lead to impaired visual responses and photoreceptor cell degeneration that ultimately cause loss of visual function. Results Therefore, studying and identifying mechanisms involved in facilitating and maintaining proper protein transport in photoreceptor cells would help our understanding of pathologies involving retinal cell degeneration in inherited retinal dystrophies, age-related macular degeneration, and Usher Syndrome. Conclusions Our mini-review will discuss mechanisms of protein transport within photoreceptors and introduce a novel role for an unconventional motor protein, MYO1C, in actin-based motor transport of the visual chromophore Rhodopsin to the OS, in support of phototransduction and visual function.
40-min nap opportunity attenuates heart rate and perceived exertion and improves physical specific abilities in elite basketball players

ABSTRACT The effect of a 40-min nap opportunity on physiological responses and specific abilities was investigated. Twelve high-level professional basketball players (26.33±5.2 years; 193.17±7.1 m; 87.48±11.2 kg) undertook randomly 40-min nap opportunity (NAP) and control condition (CON). Wellness (Hooper Index) and Epworth Sleepiness Scale (ESS) were measured before and after both conditions. Defensive (DA) and offensive (OA) agility and upper body power (UBP) were assessed after both conditions. Shooting skill (SST) performance was evaluated prior and after a fatiguing task (FT). Heart rate (HR) and rating of perceived exertion (RPE) were recorded during SST-test, FT and SST-retest. ESS, Hooper’s stress and fatigue score were significantly lower after nap compared to those before nap (0.009 ≤ p ≤ 0.03). Better performance was obtained in NAP compared to CON condition for DA, OA and UBP (0.0005 ≤ p ≤ 0.02). SST performance was significantly higher in NAP compared to CON in the retest session (p = 0.003, Δ = 20.2%). The improved performance was associated with significant lower HRpeak (p = 0.01, Δ = 5.25%) and RPE (p = 0.003, Δ = 15.12%). In conclusion, NAP reduced sleepiness and stress and fatigue and enhances physical outcomes of specific skills in elite basketball players.
Cadaveric investigation of the spread of the thoracoabdominal nerve block using the perichondral and modified perichondral approaches

the field of anesthesia. While several novel plane blocks have been described, cadaveric studies on the spread of novel blocks are important for determining appropriate applications [1]. Recently, Tulgar et al. [2] defined the thoracoabdominal nerve block using a perichondral approach (TAPA). They reported that local anesthetic (LA) administered on the upper and lower aspect of the 9th through the 10th costal cartilages would block both the anterior and lateral cutaneous branches, thus providing abdominal analgesia. After describing the TAPA, the authors also redefined the approach, naming it the modified TAPA (M-TAPA). They reported that administering LA only to the lower surface of the costal cartilage would provide successful analgesia similar to that provided by the TAPA [3]. In the literature, there are some case reports and observational studies on the TAPA and M-TAPA [2,3]; however, to the best of our knowledge, no reliable cadaveric investigation has demonstrated the spread of these blocks. Therefore, in this cadaveric investigation, we aimed to evaluate the areas of spread associated with the TAPA and M-TAPA. This study was approved by the Istanbul Medipol University Ethics and Research Committee (Decision No. 36, 06.01.2022). One fresh human male cadaver was obtained from Istanbul Medipol University. Injections were performed by two investigators with 10 and 20 years of experienced in administering regional anesthesia. With the cadaver in the supine position, the M-TAPA was performed on the right side, and the TAPA was performed on the left side. The blocks were performed under ultrasound guidance using a linear transducer. The transducer was placed at the costochondral angle in the sagittal view and then advanced to view the lower side of the chondrium. For the TAPA, 20 ml of 0.25% methylene blue dye was injected into both the upper and lower sides of the chondrium (40 ml total). For the M-TAPA, 40 ml of 0.25% methylene blue dye was injected into the lower side of the chondrium. An anatomical dissection was performed 30 min after the procedure. For both the TAPA and M-TAPA, the dye had spread over the lower surface of the upper part of the rectus abdominis and over the thoracoabdominal nerve on both sides. The lower surface of the external abdominal oblique muscle (EAOM) was completely stained with the dye (over the 8th, 9th, and 10th ribs), and so were the upper and lower surfaces of the internal abdominal oblique muscle (IAOM). Additionally, the dye had spread over the upper surface of the costal margin and from T4 to T11–T12 on both sides. However, the dye spread over the transverse abdominis muscle (TAM) to a greater degree with the M-TAPA compared with the TAPA (limited to the upper part of the muscle) (Figs. 1A and 1B). Received: March 1, 2022 Revised: March 28, 2022 (1st); April 13, 2022 (2nd); April 20, 2022 (3rd) Accepted: April 22, 2022