Miracle-dz/UniFAR-FTUs huggingface dataset:
On the value of preprints: An early career researcher perspective

Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value. The current peer-review process can lead to long delays between submission and publication, with cycles of rejection, revision, and resubmission causing redundant peer review. This situation creates unique challenges for early career researchers (ECRs), who rely heavily on timely publication of their work to gain recognition for their efforts. Today, ECRs face a changing academic landscape, including the increased interdisciplinarity of life sciences research, expansion of the researcher population, and consequent shifts in employer and funding demands. The publication of preprints, publicly available scientific manuscripts posted on dedicated preprint servers prior to journal-managed peer review, can play a key role in addressing these ECR challenges. Preprinting benefits include rapid dissemination of academic work, open access, establishing priority or concurrence, receiving feedback, and facilitating collaborations. Although there is a growing appreciation for and adoption of preprints, a minority of all articles in life sciences and medicine are preprinted. The current low rate of preprint submissions in life sciences and ECR concerns regarding preprinting need to be addressed. We provide a perspective from an interdisciplinary group of ECRs on the value of preprints and advocate their wide adoption to advance knowledge and facilitate career development.
Pasteurella multocida wound infection transmitted by a pet dog.

Introduction Human pasteurellosis is a severe human infection that accounts for 20-30 human deaths annually worldwide. Mucous secretions derived from pets comprise the primary source of infection, which are transmitted through animal scratches or bites. Case report We describe a case of Pasteurella multocida wound infection in an immunocompetent adult with a decubitus ulcer of the lower extremity. The organism was also isolated from an oral swab of the patient's dog with which he reported close contact. The patient had a favorable outcome following aggressive surgical debridement, antimicrobial treatment and subsequent wound care. Conclusion Our case illustrates that licking of open wound is an alternative source of infections by Pasteurella multocida, and emphasizes the need for avoidance of wound contact with animals.
Increased Occurrence of Target Spot of Soybean Caused by Corynespora cassiicola in the Southeastern United States.

Target spot of soybean (Glycine max (L.) Merr. ) caused by Corynespora cassiicola (Berk. & Curt.), although found in most soybean-growing countries, is considered to be a disease of limited importance (1) and has never been reported to cause soybean yield loss in the southeastern United States (2,3). Soybean plants submitted to the North Carolina Plant Disease and Insect Clinic (NCPDIC) in August 2004 from Beaufort, Robeson, Wilson, and Johnston counties, NC had symptoms consistent with target spot. Symptoms consisted of roughly circular, necrotic leaf lesions from minute to 11 mm in diameter, though typically approximately 4 to 5 mm in diameter, and with a yellow margin. Large lesions occasionally exhibited a zonate pattern often associated with this disease. Microscopic examination of the lesions revealed the presence of spores (conidia) typical of C. cassiicola (1). Conidia were mostly three to five septate with a central hilum at the base and ranged in size from 7 to 22 wide × 39 to 520 μm long. Three commercial soybean fields near Blackville, SC (Barnwell County) were severely affected by this disease and it caused premature defoliation. Nineteen of twenty-seven maturity group VII and VIII genotypes in the 2004 Clemson University soybean variety trial near Blackville, SC had visible symptoms of target spot. Heavy rainfall associated with hurricanes during September 2004 probably enhanced the incidence of this disease, and yield suppression due to target spot was estimated at 20 to 40% in some fields. In 2005, 20 of 161 soybean samples submitted to the NCPDIC or collected in surveys from 16 counties were positive for target spot on the basis of microscopic examination. Target spot also was diagnosed in six counties (Baldwin, DeKalb, Elmore, Fayette, Macon, and Pickens) in Alabama and in four additional counties (Bamberg, Hampton, Orange-burg, and Calhoun) in South Carolina in 2005. Records from the NCPDIC indicate that target spot had not been diagnosed on soybean in North Carolina since 1981. The large increase in incidence of target spot in the southeast may be related to changes in weather patterns, changes in pathogen virulence, and/or the introduction of more susceptible host genotypes. References: (1) J. B. Sinclair. Target spot. Page 27 in: Compendium of Soybean Diseases. G. L. Hartman et al. eds. The American Phytopathological Society, St. Paul, MN, 1999. (2) J. A. Wrather et al. Plant Dis. 79:1076. 1995. (3) J. A. Wrather et al. On-line publication. doi:10.1094/PHP-2003-0325-01-RV. Plant Health Progress, 2003.
Minimal important differences for improvement in shoulder condition patient-reported outcomes: a systematic review to inform a BMJ Rapid Recommendation

Objectives To identify credible anchor-based minimal important differences (MIDs) for patient-reported outcome measures (PROMs) relevant to a BMJ Rapid Recommendations addressing subacromial decompression surgery for shoulder pain. Design Systematic review. Outcome measures Estimates of anchor-based MIDs, and their credibility, for PROMs judged by the parallel BMJ Rapid Recommendations panel as important for informing their recommendation (pain, function and health-related quality of life (HRQoL)). Data sources MEDLINE, EMBASE and PsycINFO up to August 2018. Study selection and review methods We included original studies of any intervention for shoulder conditions reporting estimates of anchor-based MIDs for relevant PROMs. Two reviewers independently evaluated potentially eligible studies according to predefined selection criteria. Six reviewers, working in pairs, independently extracted data from eligible studies using a predesigned, standardised, pilot-tested extraction form and independently assessed the credibility of included studies using an MID credibility tool. Results We identified 22 studies involving 5562 patients that reported 74 empirically estimated anchor-based MIDs for 10 candidate instruments to assess shoulder pain, function and HRQoL. We identified MIDs of high credibility for pain and function outcomes and of low credibility for HRQoL. We offered median estimates for the systematic review team who applied these MIDs in Grading of Recommendations Assessment, Development and Evaluation (GRADE) evidence summaries and in their interpretations of results in the linked systematic review addressing the effectiveness of surgery for shoulder pain. Conclusions Our review provides anchor-based MID estimates, as well as a rating of their credibility, for PROMs for patients with shoulder conditions. The MID estimates inform the interpretation for a linked systematic review and guideline addressing subacromial decompression surgery for shoulder pain, and could also prove useful for authors addressing other interventions for shoulder problems. PROSPERO registration number CRD42018106531.
PD-L1 Expression Reveals Significant Association With Squamous Differentiation in Upper Tract Urothelial Carcinoma

OBJECTIVES Limited literature is available on the tumor microenvironment (TM) of upper tract urothelial carcinoma (UTUC). This study comprehensively reviews programmed death 1 receptor (PD-1)-positive and CD8+ tumor-infiltrating lymphocytes (TILs) and programmed death ligand 1 (PD-L1) expression on tumor epithelium (TE). METHODS Seventy-two nephroureterectomy specimens were analyzed for PD-L1, PD-1, and CD8. One percent or more tumor and lymphohistiocyte PD-L1 expression was considered positive. TIL density by H&E was scored semiquantitatively from 0 to 3, and CD8+ and PD-1+ TILs were quantified in hotspots. RESULTS Of the cases, 37.5% demonstrated PD-L1+ on TE. PD-L1+ TE showed an association with pathologic stage (P = .01), squamous differentiation (SqD) (P < .001), TILs by H&E (P = .02), PD-1+ peritumoral TILs (P = .01), and PD-L1+ peritumoral lymphohistiocytes (P = .002). Finally, there was a significant difference in PD-1+ peritumoral TILs in cases with SqD vs no SqD (P = .03). CONCLUSIONS Aggressive UTUC is associated with a distinct TM. Furthermore, TM of UTUC-SqD was distinctly different from those with no SqD, warranting study in a larger cohort.
Time Course of Aldehyde Oxidase and Why It Is Nonlinear

Many promising drug candidates metabolized by aldehyde oxidase (AOX) fail during clinical trial owing to underestimation of their clearance. AOX is species-specific, which makes traditional allometric studies a poor choice for estimating human clearance. Other studies have suggested using half-life calculated by measuring substrate depletion to measure clearance. In this study, we proposed using numerical fitting to enzymatic pathways other than Michaelis-Menten (MM) to avoid missing the initial high turnover rate of product formation. Here, product formation over a 240-minute time course of six AOX substrates—O6-benzylguanine, N-(2-dimethylamino)ethyl)acridine-4-carboxamide, zaleplon, phthalazine, BIBX1382 [N8-(3-Chloro-4-fluorophenyl)-N2-(1-methyl-4-piperidinyl)-pyrimido[5,4-d]pyrimidine-2,8-diamine dihydrochloride], and zoniporide—have been provided to illustrate enzyme deactivation over time to help better understand why MM kinetics sometimes leads to underestimation of rate constants. Based on the data provided in this article, the total velocity for substrates becomes slower than the initial velocity by 3.1-, 6.5-, 2.9-, 32.2-, 2.7-, and 0.2-fold, respectively, in human expressed purified enzyme, whereas the Km remains constant. Also, our studies on the role of reactive oxygen species (ROS), such as superoxide and hydrogen peroxide, show that ROS did not significantly alter the change in enzyme activity over time. Providing a new electron acceptor, 5-nitroquinoline, did, however, alter the change in rate over time for mumerous compounds. The data also illustrate the difficulties in using substrate disappearance to estimate intrinsic clearance.
The Effects of Criminal Punishment on Medical Practices in the Medical Environment

Recently, there have been cases in which doctors were criminally convicted for misdiagnosing a patient with constipation who then died of diaphragmatic hernia. The criminal punishment of doctors could create a side effect of reduced medical practitioners. This study analyzed the impact of medical disputes and deduced a plan to create a stable composition of the medical environment. An online survey was conducted with 79,022 doctors who are members of the Korea Medical Association. A total of 3109 responses were obtained, and the analysis used the questionnaire system of the Doctor’s News online survey system. The results demonstrated that doctors have become more psychologically inclined to prescribe overtreatments, avoidance treatments, and defensive treatments. Also, it was found that specialized agencies for medical appraisals were necessary. In order to resolve medical disputes objectively, it is necessary to improve credibility by securing the expertise of the Korea Medical Dispute Mediation and Arbitration Agency. In addition, there is a need for specialized agencies to undertake the medical appraisals and training of medical staff to build up their understanding of medical disputes. Thus, medical disputes can be minimized, and the fairness of medical dispute results can be strengthened.
Thermal Jeans Fragmentation within ∼1000 au in OMC-1S

We present subarcsecond 1.3 mm continuum ALMA observations toward the Orion Molecular Cloud 1 South (OMC-1S) region, down to a spatial resolution of 74 au, which reveal a total of 31 continuum sources. We also present subarcsecond 7 mm continuum VLA observations of the same region, which allow further study of fragmentation down to a spatial resolution of 40 au. By applying a method of “mean surface density of companions” we find a characteristic spatial scale at ∼560 au, and we use this spatial scale to define the boundary of 19 “cores” in OMC-1S as groupings of millimeter sources. We find an additional characteristic spatial scale at ∼2800 au, which is the typical scale of the filaments in OMC-1S, suggesting a two-level fragmentation process. We measured the fragmentation level within each core and find a higher fragmentation toward the southern filament. In addition, the cores of the southern filament are also the densest cores (within 1100 au) in OMC-1S. This is fully consistent with previous studies of fragmentation at spatial scales one order of magnitude larger, and suggests that fragmentation down to 40 au seems to be governed by thermal Jeans processes in OMC-1S.
Methyl B12 protects PC12 cells against cytotoxicity induced by Aβ25−35

Alzheimer's disease (AD) is the most common aging‐associated dementia. The population of AD patients is increasing as the world age grows. Currently, there is no cure for AD. Given that methyl vitamin B12 (methylcobalamin) deficiency is related to AD and Aβ‐induced oxidative damage and that methylcobalamin can scavenge reactive oxygen species (ROS) by direct or indirect ways, we studied the effect of methylcobalamin on the cytotoxicity of Aβ. PC12 cells were chronically exposed (24 hours) to Aβ25‐35 (25 μM) to establish an AD cell model. The cells were pretreated with or without methylcobalamin (1‐100 μM) to investigate the role of methylcobalamin. Cell viability and apoptosis were tested, followed by testing of mitochondrial damage, oxidative stress, and mitochondrial calcium concentration. We observed that methylcobalamin improved the cell viability by decreasing the ratio of apoptosis cells in this AD cell model. Further experiments suggested that methylcobalamin functioned as an antioxidant to scavenge ROS, reducing the endoplasmic reticulum‐mitochondria calcium flux through IP3R, preventing mitochondria dysfunction, ultimately protecting cells against apoptosis and cell death. Taken together, our results presented, for the first time, that methyl vitamin B12 can protect cells from Aβ‐induced cytotoxicity and the mechanism was mainly relevant to the antioxidative function of methyl B12.
Racial and Income Disparities in Health-Related Quality of Life among Smokers with a Quit Attempt in Louisiana

Background and objectives: Smoking is associated with a lower health-related quality of life (HRQOL). However, there is little information about the association between HRQOL in relation to race, income, and smoking status. The present study aimed to assess the association between HRQOL and smoking status for those of different races and income levels. Materials and Methods: This study applied a cross-sectional design using data from the 2017 patient survey of the Louisiana Tobacco Control Initiative. We obtained 1108 responses from patients at eight Louisiana public hospitals. The EuroQol (EQ-5D) US index score assessed HRQOL. Smoking status was classified into four groups: never smoked, former smoker, current smoker with a quit attempt, and current smoker without a quit attempt. Multivariate linear regression analyses were used to estimate the HRQOL for black or African Americans and whites. Results: The patients were predominantly black or African American (58.9%) with lower-income (71.2%). Bivariate analyses showed that there were differences in income levels between black or African Americans and whites (p = 0.006). Moreover, black or African Americans (median = 0.80) had a higher mean of HRQOL than whites (median = 0.76). Among lower-income black or African Americans, current smokers with a quit attempt had a lower HRQOL than current smokers (coefficient = −0.12; p < 0.01). Conclusions: Racial and income disparities were evident with regards to HRQOL, with lower-income black or African Americans who were current smokers with a quit attempt having a lower HRQOL. Intervention programs for smoking cessation should target lower-income black or African American smokers who have a prior quit attempt and provide effective cessation services to help them quit smoking and improve their HRQOL.
Psychometric Properties of Two Brief Versions of Cognitive, Insomnia-Specific Measures: The Anxiety and Preoccupation About Sleep Questionnaire and the Sleep-Associated Monitoring Index

Aim The purpose of this study was to examine the psychometric properties of two brief versions of previously validated cognitive process measures in insomnia: the Anxiety and Preoccupation about Sleep Questionnaire and the Sleep-Associated Monitoring Index. Methods Two samples (168 students and 219 patients with insomnia disorder) completed original and brief versions of the two measures (Anxiety and Preoccupation about Sleep Questionnaire-Brief version and Sleep-Associated Monitoring Index-Brief version). Also, they filled out sociodemographic questions, sleep items, and the Insomnia Severity Index. Results In both samples, the internal consistencies of the two brief versions were acceptable at α = . 70 to.72. The correlations between the original and brief versions were significant at . 79 to . 82. The two brief versions were also significantly associated with insomnia severity and nighttime symptomatology. In the student sample, those with likely insomnia disorder (14.9% of the sample) scored significantly higher on the two brief versions, relative to those without insomnia. Conclusion The two brief versions, Anxiety and Preoccupation about Sleep Questionnaire-Brief version and Sleep-Associated Monitoring Index-Brief version, displayed acceptable psychometric properties. This implies that the two brief versions might be viable alternatives for use in clinical and research settings.
First Report of Phytophthora ramorum on Canyon Live Oak in California.

During August 2002, Phytophthora ramorum S. Werres & A.W. A.M. de Cock was isolated from branches <2.0 cm in diameter on a canyon live oak (Quercus chrysolepis) in Mt. Tamalpais State Park, Marin County, CA. The shrub was a cluster of stems <1 m in diameter and 1 m high. Similar cankers were observed on small branches of adjacent canyon live oaks and there was dieback of the branches distal to the lesions. Many tanoak (Lithocarpus densiflorus), California bay laurel (Umbellularia californica), and evergreen huckleberry (Vaccinium ovatum) were also infected by P. ramorum at this site. The isolate was identified as P. ramorum by its abundant chlamydospores and caducous, semi-papillate sporangia and internal transcribed spacer (ITS) rDNA sequences identical to those of isolates of P. ramorum from Quercus spp. , tanoak, and Rhododendron (1,3). To test for pathogenicity, two greenhouse trials (5 seedlings per trial plus controls) were conducted on 20- to 24-month-old canyon live oak seedlings. Coast live oak (Q. agrifolia, section Lobatae) seedlings were included in the trials as a comparison because the species is known to be susceptible (1). Stems (approximately 1 cm in diameter) were wound inoculated (1). After 6 weeks, lesion lengths in the cambium of canyon live oak averaged 17.2 mm (range 16 to 30 mm), which was significantly greater (analysis of variance [ANOVA], P < 0.05) in both trials than those of control inoculations (mean = 6 mm). Coast live oak seedlings inoculated at the same time had mean lesion lengths of 22.6 mm (range 15 to 30 mm). P. ramorum was recovered from 100% of inoculated stems. Canyon live oak has a wide geographic range within California, but is not common in the areas currently affected by P. ramorum. We have not observed disease symptoms or unusual mortality on overstory canyon live oaks. Although a number of understory canyon live oaks at the site on Mt. Tamalpais were apparently infected, the long-term effect of P. ramorum infection on understory trees remains unclear. To our knowledge, this is the first report of infection by P. ramorum of an oak species outside of the section Lobatae (red oaks); canyon live oak is classified in the section Protobalanus (intermediate or golden cup oaks) (2). Oaks in the section Quercus (white oaks) have not been observed to be infected by P. ramorum in the field. References: (1) D. M. Rizzo et al. Plant Dis. 86:205, 2002. (2) P. Manos et al. Mol. Phylogenet. Evol. 12:333, 1999. (3) S. Werres et al. Mycol. Res. 105:1155, 2001.
Effect of Hip Flexion Angle on the Hamstring to Quadriceps Strength Ratio

The purpose of this study was to compare the hamstring to quadriceps ratio (H:Q) obtained from three different hip flexion angles. Seventy-three young athletes performed maximum isokinetic concentric and eccentric knee extension and flexion efforts at 60 °·s−1 and 240 °·s−1 from hip flexion angles of 90°, 60°, and 120°. The conventional (concentric to concentric), functional (eccentric to concentric) and mixed (eccentric at 30 °·s−1 to concentric torque at 240 °·s−1) H:Q torque ratios and the electromyographic activity from the rectus femoris and biceps femoris were analyzed. The conventional H:Q ratios and the functional H:Q ratios at 60 °·s−1 did not significantly differ between the three testing positions (p > 0.05). In contrast, testing from the 90° hip flexion angle showed a greater functional torque ratio at 240 °·s−1 and a mixed H:Q torque ratio compared with the other two positions (p < 0.05). The hip flexion angle did not influence the recorded muscle activation signals (p > 0.05). For the range of hip flexion angles tested, routine isokinetic assessment of conventional H:Q ratio and functional H:Q ratio at slow speed is not angle-dependent. Should assessment of the functional H:Q ratio at fast angular velocity or the mixed ratio is required, then selection of hip flexion angle is important.
Association between Nutritional Status and Mortality after Aortic Valve Replacement Procedure in Elderly with Severe Aortic Stenosis

Background: There is still a lack of data on the nutritional status of older people with aortic stenosis (AS) and the effect of poor nutrition on the occurrence of complications and mortality after an aortic valve replacement (AVR) procedure. The aim of this study was to assess the impact of selected nutritional status parameters in elderly patients with severe AS on the occurrence of postoperative complications and one-year mortality after the AVR procedure. Methods: 101 elderly patients with AS aged 74.6 ± 5.2 years who qualified for surgical treatment (aortic valve area [AVA] 0.73 ± 0.2 cm2) were enrolled in the study. A nutritional status assessment was performed before AVR surgery, and the frequency of postoperative complications occurring within 30 days of surgery was assessed. The one-year mortality rate was also captured. Results: Adverse events (both major and minor) up to 30 days occurred in 49.5% (n = 50) of the study population. Low Mini Nutritional Assessment (f-MNA) and Subjective Global Assessment (7-SGA) scores and low concentrations of total cholesterol, LDL-cholesterol, and prealbumin were associated with a higher risk of postoperative complications. The risk of complications increased 1.22 times (95% CI; 1.030–1.453; p = 0.019) with an impaired nutritional status. The annual mortality rate in the study group was 7.9%. Unintentional weight loss of >2.8% in the six months preceding surgery proved useful for predicting death within the first year after AVR surgery. Conclusions: The results indicate that poor nutritional status is an important factor affecting the adverse outcomes in elderly patients with severe aortic valve stenosis undergoing an AVR procedure.