Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of an antibiotic envelope in the prevention of major cardiac implantable electronic device infections

Abstract Background: Over the past decade, rates of cardiac implantable electronic device (CIED) related infections have increased and been associated with increased morbidity, mortality and financial burden on healthcare systems. Methods: To examine the effect of an antibacterial envelope in reducing major CIED related infections, we performed a systematic review and meta-analysis by searching PubMed/MEDLINE, CENTRAL, Google scholar and Clinicaltrials.gov for studies that examined the effect of an antibiotic envelope in reducing major related CIED infections, comprising of device-related endocarditis, systemic infection requiring systemic antibiotics and or device extraction, compared to control up till February 15th, 2020. A random-effects meta-analysis was conducted by calculating risk ratios (RR) and respective 95% confidence intervals (CI). Results: We include 6 studies that comprise of 11,897 patients, of which 5844 received an antibiotic envelope and 6053 did not. Compared with control, utilization of an antibiotic envelope at the time of procedure was associated with a significant 74% relative risk reduction in major CIED related infections among patients at high risk for infection (RR: 0.26 [95% CI, 0.08–0.85]; P = .03), while no significant reduction was observed among patients enrolled from studies with any risk for infection (RR: 0.53 [95% CI, 0.06–4.52]; P = .56). Additionally, no reduction in mortality among patients that received an envelope compared to control was observed (RR: 1.15 [95% CI, 0.53–2.50]; P = .72). Conclusion: The utilization of an antibiotic envelope at the time of device implantation or upgrade reduces major CIED infections, especially if used in patients perceived to be at higher risk for infection.
Cardiorespiratory Fitness, Physical Activity, Walking Speed, Lack of Participation in Leisure Activities, and Lung Cancer Mortality

Background Lung cancer (LC) is the most common cause of death in cancer patients. The influence of cardiorespiratory fitness (CF) and physical activity (PA) on LC mortality has not previously been investigated. Objective The aim of this study was to investigate through a meta-analysis the associations among CF, PA, walking speed, or leisure activity, and LC mortality and all-cause mortality. Methods MEDLINE and EMBASE were used to select relevant studies from January 2000 to August 2019. A total of 6 037 058 study subjects from 11 prospective cohort studies were included in this meta-analysis. Pooled relative risks were calculated using fixed and random-effects models to estimate the associations between CF and PA, and LC mortality. In addition, a subgroup analysis was conducted to investigate associations between walking speed and leisure activity, and LC morality. Results Greater than 9.45 metabolic equivalents of CF was associated with reduced LC mortality, compared with low-level CF. Participating in more than 150 minutes per week of PA reduced LC mortality. Slower and same walking speed were associated with increased all-cause mortality compared with age-matched individuals. Finally, moderately inactive and inactive levels of leisure activity increased all-cause mortality. Conclusions Moderate to high CF and PA were each associated with reduced risks of LC mortality. In addition, slower and same walking speed, and moderately inactive and inactive levels of leisure activity were each associated with increased risks of all-cause mortality. Implications for Practice Greater than 9.45 metabolic equivalents of CF, more than 150 minutes per week of PA, fast walking speed, and keeping active should be recommended to increase LC patient survivorship.
Maiasaura, a model organism for extinct vertebrate population biology: a large sample statistical assessment of growth dynamics and survivorship

Abstract Fossil bone microanalyses reveal the ontogenetic histories of extinct tetrapods, but incomplete fossil records often result in small sample sets lacking statistical strength. In contrast, a histological sample of 50 tibiae of the hadrosaurid dinosaur Maiasaura peeblesorum allows predictions of annual growth and ecological interpretations based on more histologic data than any previous large sample study. Tibia length correlates well (R2 > 0.9) with diaphyseal circumference, cortical area, and bone wall thickness, thereby allowing longitudinal predictions of annual body size increases based on growth mark circumference measurements. With an avian level apposition rate of 86.4 µm/day, Maiasaura achieved over half of asymptotic tibia diaphyseal circumference within its first year. Mortality rate for the first year was 89.9% but a seven year period of peak performance followed, when survivorship (mean mortality rate = 12.7%) was highest. During the third year of life, Maiasaura attained 36% (x = 1260 kg) of asymptotic body mass, growth rate was decelerating (18.2 µm/day), cortical vascular orientation changed, and mortality rate briefly increased. These transitions may indicate onset of sexual maturity and corresponding reallocation of resources to reproduction. Skeletal maturity and senescence occurred after 8 years, at which point the mean mortality rate increased to 44.4%. Compared with Alligator, an extant relative, Maiasaura exhibits rapid cortical increase early in ontogeny, while Alligator cortical growth is much lower and protracted throughout ontogeny. Our life history synthesis of Maiasaura utilizes the largest histological sample size for any extinct tetrapod species thus far, demonstrating how large sample microanalyses strengthen paleobiological interpretations.
Variant type and position predict two distinct limb phenotypes in patients with GLI3-mediated polydactyly syndromes

Introduction Pathogenic DNA variants in the GLI-Kruppel family member 3 (GLI3) gene are known to cause multiple syndromes: for example, Greig syndrome, preaxial polydactyly-type 4 (PPD4) and Pallister-Hall syndrome. Out of these, Pallister-Hall is a different entity, but the distinction between Greig syndrome and PPD4 is less evident. Using latent class analysis (LCA), our study aimed to investigate the correlation between reported limb anomalies and the reported GLI3 variants in these GLI3-mediated polydactyly syndromes. We identified two subclasses of limb anomalies that relate to the underlying variant. Methods Both local and published cases were included for analysis. The presence of individual limb phenotypes was dichotomised and an exploratory LCA was performed. Distribution of phenotypes and genotypes over the classes were explored and subsequently the key predictors of latent class membership were correlated to the different clustered genotypes. Results 297 cases were identified with 127 different variants in the GLI3 gene. A two-class model was fitted revealing two subgroups of patients with anterior versus posterior anomalies. Posterior anomalies were observed in cases with truncating variants in the activator domain (postaxial polydactyly; hand, OR: 12.7; foot, OR: 33.9). Multivariate analysis supports these results (Beta: 1.467, p=0.013 and Beta: 2.548, p<0.001, respectively). Corpus callosum agenesis was significantly correlated to these variants (OR: 8.8, p<0.001). Conclusion There are two distinct phenotypes within the GLI3-mediated polydactyly population: anteriorly and posteriorly orientated. Variants that likely produce haploinsufficiency are associated with anterior phenotypes. Posterior phenotypes are associated with truncating variants in the activator domain. Patients with these truncating variants have a greater risk for corpus callosum anomalies.
Combinations of (lipo)glycopeptides with β-lactams against MRSA: susceptibility insights.

BACKGROUND Increasing application of vancomycin due to the high prevalence of MRSA infections has led to the emergence of vancomycin intermediate-resistant Staphylococcus aureus (VISA) and heterogeneous VISA (hVISA). Consequently, the need for alternative therapies that target MRSA has become evident. OBJECTIVES To evaluate the synergy between (lipo)glycopeptides (LGP/GPs) (vancomycin, teicoplanin, telavancin, dalbavancin and oritavancin) and β-lactams (ceftaroline, cefepime, cefazolin and oxacillin) against MRSA, hVISA, VISA and daptomycin non-susceptible (DNS) phenotypes. METHODS Twenty randomly selected clinical MRSA strains (i.e. 5 MRSA, 5 hVISA, 5 VISA and 5 DNS) were assessed versus LGP/GPs alone and LGP/GPs in combination with β-lactams for MICs. Although verification of antibiotic potency against bacterial strains is assessed by the microbroth dilution (MBD) MIC method recommended by the CLSI, some antibiotics need modified assay conditions in order to demonstrate their optimal activity. RESULTS Addition of β-lactams reduced MIC values of LGP/GPs against all strains (up to 160-fold reduction). In general, LGPs (dalbavancin, oritavancin and telavancin) were more active (significant differences in MIC values, up to 8-fold) compared with vancomycin and teicoplanin. The majority of these combinations were bactericidal and superior to any single agent. CONCLUSIONS This report has examined the susceptibility patterns of LGP/GPs and their combination with β-lactams. Of interest, the impact of susceptibility tests (in terms of MIC plates and their surface area) on the synergistic activity in 24 h time-kill experiments was apparent for LGPs. Further clinical research is required to investigate synergy with LGP/GPs and β-lactams against these Staphylococcus strains.
Regional cerebral metabolic levels and turnover in awake rats after acute or chronic spinal cord injury

Spinal cord injury (SCI) is a common cause of disability, which often leads to sensorimotor cortex dysfunction above the spinal injury site. However, the cerebral regional effects on metabolic information after SCI have been little studied. Here, adult Sprague‐Dawley rats were divided into acute and chronic treatment groups and sham groups with day‐matched periods. The Basso, Beatte, and Bresnahan scores method were utilized to evaluate the changes in behaviors during the recovery of the animals, and the metabolic information was measured with the 1H‐observed/13C‐edited NMR method. Total metabolic concentrations in every region were almost similar in both treated groups. However, the metabolic kinetics in most regions in the acute group were significantly altered (P < .05), particularly in the cortical area, thalamus and medulla (P < .01). After long‐term recovery, some metabolic kinetics were recovered, especially in the temporal cortex, occipital cortex, and medulla. The metabolic kinetic changes revealed the alteration of metabolism and neurotransmission in different brain regions after SCI, which present evidence for the alternation of brain glucose oxidation. Therefore, this shows the significant influence of SCI on cerebral function and neuroscience research. This study also provides the theoretical basis for clinical therapy after SCI, such as mitochondrial transplantation.
Postflight Rash and Skin Sensitivity Following a Year-Long Spaceflight Mission.

BACKGROUND: While skin conditions are commonly reported in flight on the International Space Station (ISS), postflight skin complaints have generally been limited to foot sole sensitivity upon reloading after landing. In this case report, we describe the postflight skin findings in NASA's first year-long crewmember.CASE REPORT: The crewmember was a 51-yr-old astronaut who spent 340 d in space on this mission. His in-flight course was unremarkable except for medication use for congestion, likely secondary to microgravity-induced fluid shift and elevated CO₂ levels on the ISS, and an episode of contact dermatitis from electrodes for an experiment. He had a nominal landing in Kazakhstan. During his direct return to Houston, approximately 10 h after the Soyuz landing, he developed erythema and skin sensitivity in gravity-dependent areas. The skin findings persisted for 6 d and were successfully treated with nonsteroidal anti-inflammatory drugs, gabapentin, hydrotherapy, and massage.DISCUSSION: While vascular, allergic, and immunologic causes cannot be ruled out, we hypothesize that a prolonged lack of skin stimulation over the course of the year-long mission led to the crewmember's postflight rash and skin sensitivity. Previous studies have demonstrated alterations in cutaneous receptor feedback in the sole of the foot in spaceflight and, therefore, it is plausible that skin in other parts of the body can undergo similar changes if they are not stimulated as they normally would be on Earth. More work will be needed to better understand this phenomenon and test potential mitigations.Law J, Gilmore S, Kelly S. Postflight rash and skin sensitivity following a year-long spaceflight mission. Aerosp Med Hum Perform. 2020; 91(7):604-607.
Recent common origin, reduced population size, and marked admixture have shaped European Roma genomes.

The Roma Diaspora - traditionally known as Gypsies -remains amongst the least explored population migratory events in historical times. It involved the migration of Roma ancestors out-of-India through the plateaus of Western Asia ultimately reaching Europe. The demographic effects of the Diaspora - bottlenecks, endogamy, and gene flow - might have left marked molecular traces in the Roma genomes. Here, we analyze the whole genome sequence of 46 Roma individuals pertaining to four migrant groups in six European countries. Our analyses revealed a strong, early founder effect followed by a drastic reduction of ∼44% in effective population size. The Roma common ancestors split from the Punjabi population, from -Northwest India, some generations before the Diaspora started, less than 2,000 years ago. The initial bottleneck and subsequent endogamy are revealed by the occurrence of extensive Runs of Homozygosity and Identity By Descendent segments in all Roma populations. Furthermore, we provide evidence of gene flow from Armenian and Anatolian groups in present-day Roma, although the primary contribution to Roma gene pool comes from non-Roma Europeans, which accounts for more than 50% of their genomes. The linguistic and historical differentiation of Roma in migrant groups is confirmed by the differential proportion, but not a differential source, of European admixture in the Roma groups, which shows a westward cline. In the present study we found that despite the strong admixture Roma had in their diaspora, the signature of the initial bottleneck and the subsequent endogamy is still present in Roma genomes.
Phylogenetic significance of leaf micromorphology and anatomy in the tribe Mentheae (Nepetoideae: Lamiaceae)

A comparative micromorphological study of leaves was carried out on 102 species of Mentheae; 61 species were selected for the anatomical study. Mentheae possessed both amphistomatic and hypostomatic leaves. The diversity of leaf epidermal characteristics was based on the variation in morphology of epidermal cells, stomata types and trichome types. Although each characteristic on its own has rather limited systematic value, the combination of some of these features may be systematically relevant, especially for the identification of species. For example, branched multicellular nonglandular trichomes were a diagnostic characteristic for all genera investigated of the subtribe Salviinae; however, this trichome type was also observed in Hedeoma ciliolata and Neoeplingia leucophylloides of the subtribe Menthinae. Capitate glandular trichomes with pear-shaped heads were only observed in Salvia dorrii. Subsessile glandular trichomes with multicellular heads (more than ten cells) were an apomorphy for Perovskia. The anatomical leaf structure was consistent throughout the tribe. In some species, the vascular bundles in the midrib were modified into a mechanical tissue, which is an adaptation to xerophytic environments. The observed variations are discussed in an ecological context and their phylogenetic significance is evaluated. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160, 211–231.
Pediatric Resident Engagement With an Online Critical Care Curriculum During the Intensive Care Rotation*

Supplemental Digital Content is available in the text. Objectives: Residents are often assigned online learning materials as part of blended learning models, superimposed on other patient care and learning demands. Data that describe the time patterns of when residents interact with online learning materials during the ICU rotation are lacking. We describe resident engagement with assigned online curricula related to time of day and ICU clinical schedules, using website activity data. Design: Prospective cohort study examining curriculum completion data and cross-referencing timestamps for pre- and posttest attempts with resident schedules to determine the hours that they accessed the curriculum and whether or not they were scheduled for clinical duty. Residents at each site were cohorted based on two differing clinical schedules—extended duration (>24 hr) versus shorter (maximum 16 hr) shifts. Setting: Two large academic children’s hospitals. Subjects: Pediatric residents rotating in the PICU from July 2013 to June 2017. Interventions: None. Measurements and Main Results: One-hundred and fifty-seven pediatric residents participated in the study. The majority of residents (106/157; 68%) completed the curriculum, with no statistically significant association between overall curriculum completion and schedule cohort at either site. Residents made more test attempts at nighttime between 6 pm and 6 am (1,824/2,828; 64%) regardless of whether they were scheduled for clinical duty. Approximately two thirds of test attempts (1,785/2,828; 63%) occurred when residents were not scheduled to work, regardless of time of day. Forty-two percent of all test attempts (1,199/2,828) occurred between 6 pm and 6 am while off-duty, with 12% (342/2,828) occurring between midnight and 6 am. Conclusions: Residents rotating in the ICU completed online learning materials mainly during nighttime and off-duty hours, including usage between midnight and 6 am while off-duty. Increasing nighttime and off-duty workload may have implications for educational design and trainee wellness, particularly during busy, acute clinical rotations, and warrants further examination.
Severity of Verticillium Wilt, Plant Growth, and Spectral Reflectance Indices of Chile Pepper Under Periodic Flooding and No-flooding Conditions

Additional index words. Capsicum annuum, Verticillium dahliae, soil saturation Abstract. Verticillium wilt, caused by Verticillium dahliae, is an economically important disease on chile pepper (Capsicum annuum L.), which is grown primarily under furrow and drip irrigation in New Mexico. Field observations by producers indicate that Verticillium wilt is more prevalent on chile pepper grown under drip irrigation than under furrow irrigation. To test these observations, chile pepper plants at the six- to eight-leaf stage inoculated or noninoculated with V. dahliae were subjected to either periodic flooding or no-flooding conditions in the greenhouse. Plants under periodic flooding were subjected to three events of 7 day flooding and two events of no flooding over a period of 5 weeks. Differences among treatments were assessed using disease severity, plant dry weight, and spectral reflectance-based physiological indices such as moisture stress index (MSI), chlorophyll-based difference index, water band index, and photochemical reflectance index (PRI). There was a significant interaction between flooding and inoculation with respect to disease severity (P < 0.003). In plants inoculated with V. dahliae and subjected to periodic flooding, the relative treatment effect (RTE) based on disease severity was increased from 40% to 130% relative to noninoculated plants subjected to noflooding. However, under conditions of noflooding, RTE increased by '200% to 286% when plants were inoculated with V. dahliae relative to non- inoculated plants. In general, periodic flooding and inoculation with V. dahliae were accompanied by a decrease in plant dry weight as well as in the level of spectral reflectance-based physiological indices. In noninoculated plants subjected to periodic flooding, plant dry weight was reduced by '45% to 50% relative to noninoculated plants subjected to no flooding. In plants inoculated with V. dahliae and subjected to periodic flooding, reduction in plant dry weight was '46% to 60% relative to noninoculated plants subjected to no flooding. Under conditions of no flooding, plant dry weight was reduced by '33% to 52% when plants were inoculated with V. dahliae relative to noninoculated plants. Of all the spectral reflectance-based physiological indices, PRI was the most affected by flooding and inoculation. For noninoculated plants, the mean area under the curve for PRI (AUC-PRI) was decreased by '90% under periodic flooding relative to no flooding. In plants inoculated with V. dahliae and subjected to periodic flooding, reduction in AUC-PRI was '93% relative to noninoculated plants subjected to no flooding. Under conditions of no flooding, AUC-PRI was reduced by '93% when plants were inoculated with V. dahliae relative to noninoculated plants. These results showed that chile pepper growth and physiology were affected similarly by flooding and inoculation with V. dahliae. However, severity of Verticillium wilt was greater under no- flooding than under periodic flooding conditions.
Hypothesis‐free deep survival learning applied to the tumour microenvironment in gastric cancer

The biological complexity reflected in histology images requires advanced approaches for unbiased prognostication. Machine learning and particularly deep learning methods are increasingly applied in the field of digital pathology. In this study, we propose new ways to predict risk for cancer‐specific death from digital images of immunohistochemically (IHC) stained tissue microarrays (TMAs). Specifically, we evaluated a cohort of 248 gastric cancer patients using convolutional neural networks (CNNs) in an end‐to‐end weakly supervised scheme independent of subjective pathologist input. To account for the time‐to‐event characteristic of the outcome data, we developed new survival models to guide the network training. In addition to the standard H&E staining, we investigated the prognostic value of a panel of immune cell markers (CD8, CD20, CD68) and a proliferation marker (Ki67). Our CNN‐derived risk scores provided additional prognostic value when compared to the gold standard prognostic tool TNM stage. The CNN‐derived risk scores were also shown to be superior when systematically compared to cell density measurements or a CNN score derived from binary 5‐year survival classification, which ignores time‐to‐event. To better understand the underlying biological mechanisms, we qualitatively investigated risk heat maps for each marker which visualised the network output. We identified patterns of biological interest that were related to low risk of cancer‐specific death such as the presence of B‐cell predominated clusters and Ki67 positive sub‐regions and showed that the corresponding risk scores had prognostic value in multivariate Cox regression analyses (Ki67&CD20 risks: hazard ratio (HR) = 1.47, 95% confidence interval (CI) = 1.15–1.89, p = 0.002; CD20&CD68 risks: HR = 1.33, 95% CI = 1.07–1.67, p = 0.009). Our study demonstrates the potential additional value that deep learning in combination with a panel of IHC markers can bring to the field of precision oncology.