Miracle-dz/UniFAR-FTUs huggingface dataset:
Substantial intrinsic variability in chemoradiosensitivity of newly established anaplastic thyroid cancer cell-lines

Abstract Background: Well characterized human cell lines are needed for preclinical treatment studies of anaplastic thyroid cancer (ATC). Aims/Objectives: The aim was to establish, verify and characterize a panel of ATC cell lines. Material and methods: Cell lines were established from ATC fine-needle aspiration biopsies and characterized genetically and functionally regarding treatment sensitivities. Results: Eight cell lines were established in vitro and the anaplastic thyroid origin was verified. Seven of the cell lines were also grown as xenografts. The cell lines harboured complex karyotypes with modal numbers in hyperdiploid to near-pentaploid range. Five were TP53 mutated and three carried the BRAFV600E mutation. None had rearrangements of RET. For doxorubicin, IC50 ranged from 0.42 to 46 nmol/L and for paclitaxel from 1.6 to 196 nmol/L. Radiation sensitivity varied between 2.6 and 6.3 Gy. Two of the BRAF mutated cell lines displayed high sensitivity to vemurafenib, while the third was similar to the wild-type ones. Conclusions and significance: We describe a series of new ATC cell lines demonstrating large heterogeneity in the response to cytostatic drugs and the BRAF inhibitor vemurafenib. The observations are relevant to future attempts to optimize treatment combinations for ATC.
“Tobacco and Water”: Testing the Health Halo Effect of Natural American Spirit Cigarette Ads and Its Relationship with Perceived Absolute Harm and Use Intentions

ABSTRACT In 2015, the FDA formally warned Santa Fe Natural Tobacco Company that their “natural” and “additive-free” claims for its Natural American Spirit cigarettes conveyed reduced harm to consumers. In a settlement, Santa Fe was allowed to continue using the word “natural” in the brand name and the phrase “tobacco and water”. The company also uses eco-friendly language and plant imagery and these tactics have also been shown to communicate reduced product harm. In this study, we propose the health halo effect as an overarching framework for explaining how these ad tactics mislead consumers in an effort to provide more comprehensive guidance for regulatory action. In a between-subjects experiment, 1,577 US young adults, ages 18–24, were randomly assigned to view one of five Natural American Spirit cigarette ads featuring either: 1) eco-friendly language; 2) plant imagery; 3) the phrase “tobacco and water”; 4) all of these tactics; or 5) a control condition featuring none of these tactics. In line with past research, ads with the phrase “tobacco and water” or with all the tactics together (vs. control) created a health halo effect, increasing perceptions that Natural American Spirit cigarettes were healthier and had less potential to cause disease; these tactics also had an indirect positive effect on smoking intentions through reduced perceptions of the brand’s potential to cause disease and perceived absolute harm. Inconsistent with prior work, the eco-friendly language and plant imagery (vs. control) reduced healthfulness perceptions, increased perceptions of absolute harm, and had an indirect negative effect on smoking intentions. We contribute to past research showing that Natural American Spirit cigarette ad tactics mislead consumers. Inconsistent findings are explained in terms of stimuli design and processing of message features, indices of relative message persuasiveness, and multiple versus single-message designs.
Impact of opioid dose escalation on pain intensity: a retrospective cohort study.

Prescribers are often confronted with the decision to escalate opioid doses to achieve adequate analgesia. Understanding the impact of dose escalation on pain intensity is warranted. Using a retrospective cohort study design, Veterans with chronic pain and chronic opioid therapy were identified. Opioid dose escalators (>20% increase in average morphine milligram equivalent [MME] daily dose) were compared to dose maintainers (±20% change in average MME daily dose) assessed over two consecutive 6 month windows. Pain intensity was measured by the Numeric Rating Scale (NRS). The primary analyses used linear repeated measures models among a 1:1 matched sample of escalators and maintainers matched on propensity score and within ±180 days of the index date. Sensitivity analyses were conducted using adjusted linear repeated measures models with and without incorporating stabilized inverse probability of treatment weighting (SIPTW). There were 32,420 dose maintainers and 20,767 dose escalators identified with 19,358 (93%) matched pairs. Pain scores were persistently higher among dose escalators at each 90 day time period after the index date (0-90 Days After Index Date: Dose Escalators:4.68, 95%CI: 4.64, 4.72 Dose Maintainers:4.32, 95%CI: 4.28, 4.36, p<0.0001; 91-180 Days After Index Date: Dose Escalators:4.53, 95%CI: 4.49, 4.57; Dose Maintainers:4.25, 95%CI: 4.22, 4.29, p<0.0001) but were not different in the 90 days prior to the index date (Dose Escalators:4.64, 95%CI: 4.61, 4.68; Dose Maintainers:4.59, 95%CI: 4.55, 4.63, p=0.0551). Sensitivity analyses provided similar results as the primary analyses. Opioid dose escalation among patients with chronic pain is not associated with improvements in NRS pain scores.
Reassembling green fluorescent protein for in vitro evaluation of trans-translation

Abstract In order to discover new antibiotics with improved activity and selectivity, we created a reliable in vitro reporter system to detect trans-translation activity, the main mechanism for recycling ribosomes stalled on problematic messenger RNA (mRNA) in bacteria. This system is based on an engineered tmRNA variant that reassembles the green fluorescent protein (GFP) when trans-translation is active. Our system is adapted for high-throughput screening of chemical compounds by fluorescence.
Association between serum choline and betaine concentrations and longitudinal changes of body composition in community-dwelling middle-aged and older Chinese adults.

Previous studies suggested that betaine and choline may be beneficial for body composition. But no longitudinal study has been conducted to illustrate whether choline and betaine have long-term effects on changes in body composition. This study aimed to prospectively investigate the association between serum choline and betaine concentrations and 3-year changes in body composition in community-dwelling Chinese adults. This present analysis used data from 1384 women and 554 men aged 40-75 years. Serum concentrations of betaine and choline at baseline were assessed using HPLC-MS. Body composition parameters, i.e. muscle mass (MM), fat mass (FM) and body fat percentage (FM%), were measured using dual-energy X-ray absorptiometry at the first and the second follow-ups. After adjustment for potential cofounders, higher serum choline concentrations was associated with a lower decrease in MM in men (β=0.022, P=0.025) and a less increase in FM and FM% in women with baseline choline concentrations below 21.5 μmol/L (all P for non-linearity=0.007); higher serum betaine concentrations were associated with a lower decline in MM and a less increase in FM and FM% among men whose betaine concentrations were lower than 55 μmol/L (all P for non-linearity＜0.05). These findings suggest that higher concentrations of serum choline and betaine may be associated with favorable changes in body composition profiles among men and women who have relatively low concentrations, especially in men. Novelty bullets: ●Higher concentrations of serum choline and betaine were associated with favorable changes in body composition. ●Such favorable associations were more pronounced in men.
The Efficacy of Extracorporeal Shock Wave Therapy for Chronic Coccydynia

Objective: Coccydynia is a disorder that decreases quality of life with significant functional failure. Extra-corporeal shock wave therapy (ESWT) is used to treat several painful musculoskeletal disorders. Subjects and Methods: The medical records of 34 patients (29 females, 5 males) who had been treated with ESWT between 2017 and 2018 for chronic coccydynia were evaluated. Visual analog scale (VAS) scores were noted at the initial consultation, at each session, and during the initial and follow-up (at 6 months) examinations after the treatment. The 36-item short form (SF-36) quality of life scale survey was conducted at the beginning and end of the treatment. MRI was performed before the start of the procedure and 1 month after the end of the treatment. Results: The mean VAS score was 9.6 (9–10) before the treatment and 3.4 (0–2) after the treatment (p < 0.05). The VAS score decreased to ≤3 in 79.4% of patients. Bone marrow edema regressed in 6% of patients. Significant improvement was observed in all of the SF-36 parameters, except for two. Conclusion: In our patient group, ESWT provided effective pain control. In order to evaluate the efficacy of ESWT more accurately and sensitively, prospective randomized studies with longer follow-up periods, in which ESWT is compared with different energy doses and different treatment methods, are needed.
Complete Genome Sequences of 13 Bacillus subtilis Soil Isolates for Studying Secondary Metabolite Diversity

Bacillus subtilis is a plant-benefiting soil-dwelling Gram-positive bacterium with secondary metabolite production potential. Here, we report the complete genome sequences of 13 B. subtilis strains isolated from different soil samples in Germany and Denmark. ABSTRACT Bacillus subtilis is a plant-benefiting soil-dwelling Gram-positive bacterium with secondary metabolite production potential. Here, we report the complete genome sequences of 13 B. subtilis strains isolated from different soil samples in Germany and Denmark.
Personal electronic healthcare records: What influences consumers to engage with their clinical data online? A literature review

Background: Online electronic records such as patient portals and personally controlled electronic health records (PEHRs) have been widely viewed as a key component to modernising the delivery of healthcare but the uptake of such systems has been slow. Objective: The purpose of this literature review was to determine what influences consumers to engage and interact with their clinical data online. Method: A scoping literature review following PRISMA guidelines was completed. Electronic patient record research published between January 2009 and December 2018 was included. Following screening and full-text reviews, a total of 64 records were included in this review. Results: Three key areas of influence on consumer engagement with their clinical data online emerged: demographic factors affecting consumer interaction with PEHRs; consumers’ perceived benefits and detriments of PEHR use; and the influence of PEHR use on consumer empowerment and responsibility. Discussion: Consumer motivation and readiness for engaging with their clinical data online and their long-term ongoing use of these systems requires further exploration. Conclusion: As worldwide rates of consumer interactions with individual online clinical data remain low, what influences consumer engagement with a PEHR remains unknown. Further research into the consumer perspective of, and interaction with, a PEHR, needs to be undertaken to determine if factors such as frequent usage of the system by consumers leads to improved clinical outcomes.
Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages

Leuconostoc carnosum is a lactic acid bacterium that preferentially colonizes meat. In this work, we present the draft genome sequences of 12 Leuconostoc carnosum strains isolated from modified-atmosphere-packaged cooked ham and fresh sausages. Three strains harbor bacteriocin genes. ABSTRACT Leuconostoc carnosum is a lactic acid bacterium that preferentially colonizes meat. In this work, we present the draft genome sequences of 12 Leuconostoc carnosum strains isolated from modified-atmosphere-packaged cooked ham and fresh sausages. Three strains harbor bacteriocin genes.
Evaluating symptom burden in kidney transplant recipients: validation of the revised Edmonton Symptom Assessment System for kidney transplant recipients – a single‐center, cross‐sectional study

We assessed the validity of the Edmonton Symptom Assessment System (ESAS‐r) in kidney transplant recipients (KTR). A cross‐sectional sample of 252 KTR was recruited. Individual ESAS‐r symptom scores and symptom domain scores were evaluated. Internal consistency, convergent validity, and construct validity were assessed with Cronbach’s α, Spearman’s rank correlations, and a priori‐defined risk group comparisons. Mean (SD) age was 51 (16), 58% were male, and 58% Caucasian. ESAS‐r Physical, Emotional, and Global Symptom Scores demonstrated good internal consistency (α > 0.8 for all). ESAS‐r Physical and Global Symptom Scores strongly correlated with PHQ‐9 scores (0.72, 95% CI: 0.64–0.78 and 0.74, 95% CI: 0.67–0.80). For a priori‐defined risk groups, individual ESAS‐r symptom score differed between groups with lower versus higher eGFR [pain: 1 (0–3) vs. 0 (0–2), delta = 0.18; tiredness: 3 (1–5) vs. 1.5 (0–4), delta = 0.21] and lower versus higher hemoglobin [tiredness: 3 (1–6) vs. 2 (0–4), delta = 0.27]. ESAS‐r Global and Physical Symptom Scores differed between groups with lower versus higher hemoglobin [13 (6–29) vs. 6.5 (0–18.5), delta = 0.3, and 9 (2–19) vs. 4 (0–13), delta = 0.24] and lower versus higher eGFR [11 (4–20) vs. 6.5 (2–13), delta = 0.21, and 7 (2–16) vs. 3 (0–9), delta = 0.26]. These data support reliability and construct validity of ESAS‐r in KTR. Future studies should explore its clinical utility for symptom assessment among KTR.
Binge eating and binge-eating disorder in Black women: A systematic review.

OBJECTIVE Although several effective behavioral treatments for binge-eating disorder (BED) exist, there are racial disparities in treatment access, with African-Americans and/or Black individuals having some of the lowest rates of access to care. Little is known about the experience and treatment of binge eating (BE) and BED among Black women. METHOD This systematic review, conducted according to PRISMA guidelines, synthesizes information related to BE and BED in Black women. RESULTS A total of N = 38 studies met our eligibility criteria. We did not identify any systematic risk of bias across studies. The majority of included studies used cross-sectional survey methodology, and relied on interview (EDE) and self-report measures (particularly the Binge Eating Scale, BES) for the assessment of BE. Outcomes were inconsistently measured across trials, and there are limited data on the results of evidence-based treatments for BE/BED in Black women. DISCUSSION Although Black women have similar or higher rates of BE than White women, most research on BE and BED has focused on White women, with Black individuals underrepresented in clinical trials. Future research should examine evidence-based treatments to prevent and treat BED in this population. OBJETIVO Aunque existen varios tratamientos conductuales que son efectivos para el Trastorno de Atracones (BED, por sus siglas en inglés), existen disparidades raciales en el acceso a tratamiento, con individuos Afroamericanos y/o personas de color teniendo algunas de las tasas más bajas de acceso al cuidado de la salud. Se sabe muy poco acerca de la experiencia y tratamiento del comer en atracones (BE, por sus siglas en inglés) y BED entre mujeres afroamericanas y/o de color. MÉTODO: Esta revisión sistemática, realizada bajo lineamientos de las guías PRISMA, sintetiza información relacionada con BE y BED en mujeres afroamericanas y/o de color. RESULTADOS Un total de N = 38 estudios cumplieron con nuestros criterios de elegibilidad. No identificamos ningún riesgo sistemático de sesgo entre los estudios. La mayoría de los estudios incluidos utilizaron una metodología de encuesta transversal y se basaron en la entrevista (EDE) y las medidas de autoinforme (en particular, la Binge Eating Scale, BES) para la evaluación de BE. Los resultados se midieron de manera inconsistente entre los ensayos, y hay datos limitados sobre los resultados de los tratamientos basados en la evidencia para BE/BED en mujeres afroamericanas y/o de color. DISCUSIÓN: Aunque las mujeres afroamericanas y/o de color tienen tasas similares o más altas de BE que las mujeres blancas, la mayoría de las investigaciones sobre BE y BED se han centrado en las mujeres blancas, con individuos afroamericanos y/o de color subrepresentados en ensayos clínicos. La investigación futura debería examinar los tratamientos basados en la evidencia para prevenir y tratar el BED en esta población.
Expression of MiR-335 and its target metalloproteinase genes: clinical significance in breast cancer

Abstract Background Early diagnosis of breast cancer decreases mortality rate; therefore, novel diagnostic methods are urgently required. In this study, authors aimed to investigate the role of serum-derived miR-335 in breast cancer, and the expression of matrix metalloproteinase-2 (MMP2) and matrix metalloproteinase-9 (MMP9) and evaluating their feasibility and clinical utility as biomarkers for the early detection of breast cancer. Materials and methods Blood samples were collected from a total of 210 individuals who were enrolled in this study. The participants were divided into newly diagnosed breast cancer patients (n = 115), patients with benign breast lesions (n =55) and healthy individuals as control group (n =40). The expression profile of miR-335, MMP2 and MMP9 were determined using quantitative polymerase chain reaction (qPCR). Results MiR 335 expression level was down-regulated in primary breast cancer group as compared to benign breast group and healthy individuals with 98% and 94.9% sensitivity and specificity, respectively. MMP2 and MMP9 showed significantly higher expression levels in breast cancer group as compared to both benign and healthy group and reporting 92.7% and 93% sensitivity, respectively. The relations between investigated markers and pathologic types, staging, grading, and lymph node involvement were significant with these factors. Expression level of miR-335 was decreased with increased MMP2 and MMP9 at significant level. Conclusion MiR-335, MMP2, and MMP9 can be used as diagnostic markers in breast cancer.
Draft Genome Sequence of Lactobacillus crispatus CIP 104459, Isolated from a Vaginal Swab

We report the draft genome sequence of Lactobacillus crispatus CIP 104459, isolated from a human vaginal swab. This draft genome consists of 1,993,673 bp, with 36.8% G+C content and 2,024 predicted protein-encoding sequences. ABSTRACT We report the draft genome sequence of Lactobacillus crispatus CIP 104459, isolated from a human vaginal swab. This draft genome consists of 1,993,673 bp, with 36.8% G+C content and 2,024 predicted protein-encoding sequences.
Qualitative study of loneliness in a senior housing community: the importance of wisdom and other coping strategies

Abstract Objective Older adults are at a high risk for loneliness, which impacts their health, well-being, and longevity. While related to social isolation, loneliness is a distinct, internally experienced, distressing feeling. The present qualitative study sought to identify characteristics of loneliness in older adults living independently within a senior housing community, which is typically designed to reduce social isolation. Method Semi-structured qualitative interviews regarding the experience of loneliness, risk factors, and ways to combat it were conducted with 30 older adults, ages 65–92 years. The interviews were audiotaped, transcribed, and coded using a grounded theory analytic approach based on coding, consensus, co-occurrence, and comparison. Results Three main themes with multiple subthemes are described: (A) Risk and Protective factors for loneliness: age-associated losses, lack of social skills or abilities, and protective personality traits; (B) Experience of loneliness: Sadness and lack of meaning as well as Lack of motivation; and (C) Coping strategies to prevent or overcome loneliness: acceptance of aging, compassion, seeking companionship, and environment enables socialization. Discussion Despite living within a communal setting designed to reduce social isolation, many older adults described feeling lonely in stark negative terms, attributing it to aging-associated losses or lack of social skills and abilities. However, interviewees also reported positive personal qualities and actions to prevent or cope with loneliness, several of which mirrored specific components of wisdom. The results support the reported inverse relationship between loneliness and wisdom and suggest a potential role for wisdom-enhancing interventions to reduce and prevent loneliness in older populations.
Graft-versus-host disease reduces lymph node display of tissue-restricted self-antigens and promotes autoimmunity

Acute graft-versus-host disease (GVHD) is initially triggered by alloreactive T cells, which damage peripheral tissues and lymphoid organs. Subsequent transition to chronic GVHD involves the emergence of autoimmunity, although the underlying mechanisms driving this process are unclear. Here, we tested the hypothesis that acute GVHD blocks peripheral tolerance of autoreactive T cells by impairing lymph node (LN) display of peripheral tissue–restricted antigens (PTAs). At the initiation of GVHD, LN fibroblastic reticular cells (FRCs) rapidly reduced expression of genes regulated by DEAF1, an autoimmune regulator-like transcription factor required for intranodal expression of PTAs. Subsequently, GVHD led to the selective elimination of the FRC population, and blocked the repair pathways required for its regeneration. We used a transgenic mouse model to show that the loss of presentation of an intestinal PTA by FRCs during GVHD resulted in the activation of autoaggressive T cells and gut injury. Finally, we show that FRCs normally expressed a unique PTA gene signature that was highly enriched for genes expressed in the target organs affected by chronic GVHD. In conclusion, acute GVHD damages and prevents repair of the FRC network, thus disabling an essential platform for purging autoreactive T cells from the repertoire.
Repository-based plasmid design

There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. The challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson Assembly. It finds existing DNA sequences in user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.