Miracle-dz/UniFAR-FTUs huggingface dataset:
A Simple Technique to Correct Lumpectomy Deformities Using Free Nipple Grafting

Background Lumpectomy followed by radiation can lead to severe breast asymmetry. Many surgeons are hesitant to perform traditional mastopexies on irradiated breasts due to increased complication rates. An alternative approach to achieve breast symmetry is presented. This technique consists of free nipple-areola complex (NAC) grafting of the irradiated breast to a higher position and primary closure of the donor site, in an appropriate fashion without undermining, followed by a formal mastopexy of the nonradiated breast. Objective To evaluate the outcomes of free NAC grafting, used as an alternative method to achieve breast symmetry, in patients who underwent lumpectomy with radiation. Methods A case series of 5 patients who underwent breast revision using this technique, performed by a single surgeon from 2017 to 2019 (n = 5), is presented. Patient Demographics All patients had history of lumpectomy followed by radiation therapy. The average age was 59.2 years, average BMI was 33.0. Three of 5 patients had a significant smoking history. The average time between radiation and surgery was 5.9 years. Results The average operating time was 141.8 minutes. The average follow-up period was 5.8 months. Two (40%) of the free NAC grafts were complicated by hypopigmentation of the reconstructed NAC. No major complications were reported, and no patients required return to the operating room. All patients had successful outcomes with improved breast symmetry. Conclusions Free NAC grafting of irradiated breasts and contralateral mastopexy may be a reliable alternative to achieve breast symmetry, with a less invasive approach, in patients who underwent lumpectomy and radiation.
A cross-sectional evaluation of the relationship between social jetlag and diet quality

ABSTRACT The aim of this study was to compare anthropometric measures of obesity and sleep qualities in individuals with/without social jetlag (SJL). In addition, it was aimed to compare the energy, macronutrient intake and diet qualities of individuals with/without SJL during school and non-school days. This study comprised 710 university students with mean age 21.58 ± 1.41 years. The presence of SJL was acknowledged if there was a difference of more than 1 hour between the middle of sleep time on school day and on non-school day. While the physical activity levels (PALs) of the individuals were determined with a 24-hour physical activity record, measurements such as waist circumference, neck circumference and body mass index were recorded for anthropometric measurements. Pittsburgh Sleep Quality Index was used to determine the sleep quality of the individuals. Energy, macronutrients intake, and diet quality were calculated from the 24-h dietary recall of the individuals, and recorded for the school days and non-school days. In this study, 76% of the individuals (n = 542) were determined as exposed to SJL. Although there was no significant difference in their PALs, individuals with SJL had a higher waist (p < .05) and neck (p < .05) circumference, as well as higher body mass index (p < .05). Individuals with SJL were found to have significantly poor sleep quality (OR:1.109, p < .031) and sleep latency (OR:1.130, p < .001) after adjustment for confounding factors. When compared to school days, in the individuals with SJL, energy (p < .001), fat (p < .001), saturated fatty acids (SFA) (p < .001), and mono unsaturated fatty acids (MUFA) (p < .001) were significantly increased; however, fiber intake (p < .001) was significantly reduced on non-school days. Although there was no significant difference in the diet quality scores between the groups on the school days, the diet quality of the individuals without SJL on non-school days was increased significantly (p < .05). In conclusion, SJL was associated with sleep loss, increased body mass index, and lowered diet quality in university students.
MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences

SUMMARY Genomic sequences are widely used to infer the evolutionary history of a given group of individuals. Many methods have been developed for sequence clustering and tree building. In the early days of genome sequencing, these were often limited to hundreds of sequences, but due to the surge of high throughput sequencing, it is now common to have millions of sampled sequences at hand. We introduce MNHN-Tree-Tools, a high performance set of algorithms that builds multi-scale, nested clusters of sequences found in a FASTA file. MNHN-Tree-Tools does not rely on sequence alignment and can thus be used on large datasets to infer a sequence tree. Herein we outline two applications: A human alpha-satellite repeats classification and a tree of life derivation from 16S/18S rDNA sequences. CODE AVAILABILITY Open source with a Zlib License via the Git protocol: https://gitlab.in2p3. fr/mnhn-tools/mnhn-tree-tools. SUPPLEMENTARY INFORMATION An in depth discussion about the algorithm with numerical simulations: https://gitlab.in2p3. fr/mnhn-tools/tree-tools-algorithms-document/-/raw/master/article.pdf. MANUAL A detailed users guide and tutorial: https://gitlab.in2p3. fr/mnhn-tools/mnhn-tree-tools-manual/-/raw/master/manual.pdf. WEBSITE AND FAQ http://treetools.haschka. net.
TRDMT1 participates in the DNA damage repair of granulosa cells in premature ovarian failure

The molecular mechanisms underlying premature ovarian failure, which seriously impacts the physical and psychological health of patients, are not fully understood. Here, we present the role of TRDMT1 in reactive oxygen species-induced granulosa cells death, which is considered an important cause of premature ovarian failure. We found that reactive oxygen species were increased in a H2O2 dose-dependent manner and accompanied by the nuclear shuttling of TRDMT1, increased DNA damage and increased apoptosis of granulosa cells. In addition, reactive oxygen species-induced granulosa cells apoptosis could be prevented by the antioxidant N-acetylcysteine or overexpression of TRDMT1. Furthermore, DNA repair following reactive oxygen species induction was severely impaired/enhanced in TRDMT1 mutants, which exhibited reduced/increased RNA m5C methylation activity. Altogether, our results reveal a novel role of TRDMT1 in the regulation of premature ovarian failure through the repair of reactive oxygen species-triggered DNA damage in granulosa cells and provide an improved understanding of the mechanisms underlying granulosa cells apoptosis, which could potentially be useful for future clinical treatments of premature ovarian failure.
Efeito de condicionadores químicos sobre a qualidade da cama de frango (Effect of chemical conditioners on poultry litter quality)

The chemical quality of poultry litter submitted, for three consecutive flocks, to different chemical conditioners was evaluated. One-thousand-three-hundred and twenty birds, 440 birds per each flock, were allotted to five treatments (Treat. 1 – untreated litter; Treat. 2 – litter treated with aluminum sulfate; Treat. 3 – litter treated with gypsum; Treat. 4 – litter treated with single superphosphate and Treat. 5 – litter treated with hydrated lime) in a completely randomized block design with four replicates. Sample litters were collected at 42 days. No influence of the conditioners (P>0.05) on the dry matter results was observed. Aluminum sulfate reduced (P<0.002) pH (7.42, 7.07 and 6.00, respectively in the first, second and third flocks) and reduced (P<0.05) the quantity of volatilized ammonia (3.14, 1.36 and 1.79 mg/100g, respectively in the first, second and third flocks), in comparison to other treatments. Aluminum sulfate can be added to poultry litter to reduce pH and to inhibit the ammonia volatilization.
Inactivation of common airborne antigens by perfluoroalkyl chemicals modulates early life allergic asthma

Significance Perfluoroalkyl chemicals (PFCs) are man-made chemicals ubiquitously present in humans. We demonstrate that a major PFC, perfluorooctane sulfonate (PFOS), dampens mice from developing house dust mite (HDM)–induced asthma, while abolishing the microbial product LPS’s protective effect in asthma development. This finding has direct human relevance, considering the low-PFOS concentrations necessary for its effect. Mechanistically, PFOS binds with high affinity to Der p1, a major allergen from HDM, as well as to the lipid A moiety of LPS, resulting in their inactivation. Our data highlight that PFC exposure may play a previously unappreciated role in modulating allergic asthma and emphasize the importance of reducing exposure. Allergic asthma, driven by T helper 2 cell-mediated immune responses to common environmental antigens, remains the most common respiratory disease in children. Perfluorinated chemicals (PFCs) are environmental contaminants of great concern, because of their wide application, persistence in the environment, and bioaccumulation. PFCs associate with immunological disorders including asthma and attenuate immune responses to vaccines. The influence of PFCs on the immunological response to allergens during childhood is unknown. We report here that a major PFC, perfluorooctane sulfonate (PFOS), inactivates house dust mite (HDM) to dampen 5-wk-old, early weaned mice from developing HDM-induced allergic asthma. PFOS further attenuates the asthma protective effect of the microbial product lipopolysaccharide (LPS). We demonstrate that PFOS prevents desensitization of lung epithelia by LPS, thus abolishing the latter’s protective effect. A close mechanistic study reveals that PFOS specifically binds the major HDM allergen Der p1 with high affinity as well as the lipid A moiety of LPS, leading to the inactivation of both antigens. Moreover, PFOS at physiological human (nanomolar) concentrations inactivates Der p1 from HDM and LPS in vitro, although higher doses did not cause further inactivation because of possible formation of PFOS aggregates. This PFOS-induced neutralization of LPS has been further validated in primary human cell models and extended to an in vivo bacterial infection mouse model. This study demonstrates that early life exposure of mice to a PFC blunts airway antigen bioactivity to modulate pulmonary inflammatory responses, which may adversely affect early pulmonary health.
Pain Relief by Analgesic Eardrops: Paradigm Shift in the Treatment of Acute Otitis Media?

Abstract Acute otitis media is a common middle ear infection in children with the predominant symptoms of hearing impairment and pain. If antibiotics are given, they need time to have an effect on the inflammation, so the focus is on pain control. For pain management local anesthetics have the advantage of lesser systemic side effects but are still subject to scrutiny. In this review the literature between 2000 and 2020 was systematically searched for investigating studies and recommendation in guidelines against the background of the mode of action. 11 clinical studies, 2 guidelines and 5 reports resp. reviews could be identified. Contraindications and side effects were not found in these studies. The analgesic ear drops showed in placebo-controlled studies a relatively short duration of action when applied once but rapid onset of action. There is evidence that analgesic ear drops could provide a first-line analgesia in otitis media without systemic adverse effects such as gastrointestinal disturbance and nausea and could support an antibiotic-saving wait-and-see attitude. The review shows a change in attitude towards the recommendation to include local anesthetics ear drops in otitis media but still there is a lack in treatment protocols which go beyond a single administration. The results do not yet show a significant paradigm shift. The reviews revealed indications that a more adapted galenic preparation could give more effectiveness. Pharmaceutical research in this field should be intensified to exploit the analgesic potential of local anesthetic ear drops in acute otitis media.
The Effects of Visual Backgrounds in the Virtual Environments on the Postural Stability of Standing

A photorealistic scene in a head mount display (HMD) is considered high fidelity and associated with postural stability similar to that in the real world, but the effects of visual background under different standing conditions have not been examined. Thirty-four healthy adults performed four standing (standardized, narrow, tandem and one-leg) tasks in three scenes with an HMD, while viewing one of three scenes: a real room (real scene, RS), a photorealistic scene (VrS) and a blank scene (BS). The effects of the visual scenes and standing tasks on sway parameters were analyzed. Romberg quotients (RQs) of the sway parameters were compared between RS and VrS with reference to BS to compare visual contribution to posture stability. Sway parameters were similar during all three scenes during the standardized and narrow standing tasks, but higher in VrS and BS conditions than in the RS condition during the tandem and one-leg standing tasks. The effects of visual scenes on postural stability showed a significant interaction with the standing tasks. The BS/VsR and BS/RS ratios were close to 1.0 for the standardized and narrow standing tasks, and the magnitude of increase was lower for BS/VsR than BS/RS during the tandem and one-leg standing tasks, indicating different levels of visual dependence. The effects of virtual scenes on postural stability were task-dependent. Adjusting the amount of visual stimuli and choosing tasks with higher postural demands may result in synergic effects, but the influence of visual environments should be examined with consideration of visual targeting.
Oxygen consumption in the severe exercise intensity domain during incremental and square-wave test modes

Incremental tests are commonly used to predict metabolic responses during square-wave mode exercises. However, in some cases the predicted and observed results may be not similar. Main objective: To verify the hypothesis that, at certain intensities in the severe domain, VO2 determined during the incremental test is lower than that observed at these workloads using the square-wave test. Methodological proceedings: Eight physically active males (21.5 ± 4 years, 73.7 ± 5.3 kg and 180.8 ± 4.1 cm) performed: 1) an incremental test on cycle ergometer to determine the VO2 of the intensities (VO2INC); 2) a square-wave test at three severe intensities (Light (L), Medium (M) and Heavy (H)) to determine the critical power (CP) and to compare the VO2 (VO2RET) observed with the VO2INC; 3) a square-wave test at CP intensity to compare the time response of VO2 with P, M and L, at four different sample times. Results: The VO2INC at L intensity underestimated the VO2RET (3.2 ± 0.5 vs. 3.8 ± 0.6 l.min-1). No differences were observed at the other intensities (M: 3.5 ± 0.5 vs. 3.6 ± 0.5 l.min-1; H: 3.7 ± 0.5 vs. 3.4 ± 0.6 l.min-1; CP: 2.7 ± 0.5 vs. 3.0 ± 0.6 l.min-1). The VO2 at CP was lower at all times, exhibited a steady state and did not achieve VO2max. Initially, at L intensity, the VO2 was smaller than its pairs. However, at the last sample time, it achieved VO2max and became equal to the other severe intensities. Conclusion: The incremental test underestimates the VO2 observed at lighter intensities within the severe domain.
Impact of errors in spot size and spot position in robustly optimized pencil beam scanning proton‐based stereotactic body radiation therapy (SBRT) lung plans

Abstract Purpose The purpose of the current study was threefold: (a) investigate the impact of the variations (errors) in spot sizes in robustly optimized pencil beam scanning (PBS) proton‐based stereotactic body radiation therapy (SBRT) lung plans, (b) evaluate the impact of spot sizes and position errors simultaneously, and (c) assess the overall effect of spot size and position errors occurring simultaneously in conjunction with either setup or range errors. Methods In this retrospective study, computed tomography (CT) data set of five lung patients was selected. Treatment plans were regenerated for a total dose of 5000 cGy(RBE) in 5 fractions using a single‐field optimization (SFO) technique. Monte Carlo was used for the plan optimization and final dose calculations. Nominal plans were normalized such that 99% of the clinical target volume (CTV) received the prescription dose. The analysis was divided into three groups. Group 1: The increasing and decreasing spot sizes were evaluated for ±10%, ±15%, and ±20% errors. Group 2: Errors in spot size and spot positions were evaluated simultaneously (spot size: ±10%; spot position: ±1 and ±2 mm). Group 3: Simulated plans from Group 2 were evaluated for the setup (±5 mm) and range (±3.5%) errors. Results Group 1: For the spot size errors of ±10%, the average reduction in D99% for −10% and +10% errors was 0.7% and 1.1%, respectively. For −15% and +15% spot size errors, the average reduction in D99% was 1.4% and 1.9%, respectively. The average reduction in D99% was 2.1% for −20% error and 2.8% for +20% error. The hot spot evaluation showed that, for the same magnitude of error, the decreasing spot sizes resulted in a positive difference (hotter plan) when compared with the increasing spot sizes. Group 2: For a 10% increase in spot size in conjunction with a −1 mm (+1 mm) shift in spot position, the average reduction in D99% was 1.5% (1.8%). For a 10% decrease in spot size in conjunction with a −1 mm (+1 mm) shift in spot position, the reduction in D99% was 0.8% (0.9%). For the spot size errors of ±10% and spot position errors of ±2 mm, the average reduction in D99% was 2.4%. Group 3: Based on the results from 160 plans (4 plans for spot size [±10%] and position [±1 mm] errors × 8 scenarios × 5 patients), the average D99% was 4748 cGy(RBE) with the average reduction of 5.0%. The isocentric shift in the superior–inferior direction yielded the least homogenous dose distributions inside the target volume. Conclusion The increasing spot sizes resulted in decreased target coverage and dose homogeneity. Similarly, the decreasing spot sizes led to a loss of target coverage, overdosage, and degradation of dose homogeneity. The addition of spot size and position errors to plan robustness parameters (setup and range uncertainties) increased the target coverage loss and decreased the dose homogeneity.
Validation of the World Health Organization/ International Society of Hypertension (WHO/ISH) cardiovascular risk predictions in Sri Lankans based on findings from a prospective cohort study

Introduction and objectives There are no cardiovascular (CV) risk prediction models for Sri Lankans. Different risk prediction models not validated for Sri Lankans are being used to predict CV risk of Sri Lankans. We validated the WHO/ISH (SEAR-B) risk prediction charts prospectively in a population-based cohort of Sri Lankans. Method We selected 40–64 year-old participants from the Ragama Medical Officer of Health (MOH) area in 2007 by stratified random sampling and followed them up for 10 years. Ten-year risk predictions of a fatal/non-fatal cardiovascular event (CVE) in 2007 were calculated using WHO/ISH (SEAR-B) charts with and without cholesterol. The CVEs that occurred from 2007–2017 were ascertained. Risk predictions in 2007 were validated against observed CVEs in 2017. Results Of 2517 participants, the mean age was 53.7 year (SD: 6.7) and 1132 (45%) were males. Using WHO/ISH chart with cholesterol, the percentages of subjects with a 10-year CV risk <10%, 10–19%, 20%-29%, 30–39%, ≥40% were 80.7%, 9.9%, 3.8%, 2.5% and 3.1%, respectively. 142 non-fatal and 73 fatal CVEs were observed during follow-up. Among the cohort, 9.4% were predicted of having a CV risk ≥20% and 8.6% CVEs were observed in the risk category. CVEs were within the predictions of WHO/ISH charts with and without cholesterol in both high (≥20%) and low(<20%) risk males, but only in low(<20%) risk females. The predictions of WHO/ISH charts, with-and without-cholesterol were in agreement in 81% of subjects (ĸ = 0.429; p<0.001). Conclusions WHO/ISH (SEAR B) risk prediction charts with-and without-cholesterol may be used in Sri Lanka. Risk charts are more predictive in males than in females and for lower-risk categories. The predictions when stratifying into 2 categories, low risk (<20%) and high risk (≥20%), are more appropriate in clinical practice.
A novel self-supported porous ZnO nanobelt arrays on Zn foils: excellent binder-free anode materials for LIBs

ZnO is considered to be one of the promising anode materials for lithium-ion batteries (LIBs), but the poor electronic conductivity and large volume variation during lithium-ion extraction and insertion process of ZnO seriously hinders its commercial application in LIBs. In this study, we synthesized a novel self-supporting porous ZnO nanobelt (PZB) arrays on Zn foils, in which Zn foils can be directly used as current collectors to promote electrically connection between the active materials and the current collectors. Furthermore, the well-aligned ZnO nanobelts have a thin thickness and uniform porous structure, which endue it well improved electrochemical performance. The PZB anodes display a high areal capacity of 5.91 mAh cm−2 at current density of 0.5 mA cm−2 at room temperature, and deliver an areal capacity of 1.73 mAh cm−2 at −20 °C, indicating its excellent application potential especially at low temperatures, and it makes the porous ZnO nanobelts a practical anode material for LIBs.
Polar Growth in Corynebacterium glutamicum Has a Flexible Cell Wall Synthase Requirement

The Corynebacterineae suborder includes a number of major bacterial pathogens. These organisms grow by polar extension unlike most well-studied model bacteria, which grow by inserting wall material at dispersed sites along their length. ABSTRACT Members of the Corynebacterineae suborder of bacteria, including major pathogens such as Mycobacterium tuberculosis, grow via the insertion of new cell wall peptidoglycan (PG) material at their poles. This mode of elongation differs from that used by Escherichia coli and other more well-studied model organisms that grow by inserting new PG at dispersed sites along their cell body. Dispersed cell elongation is known to strictly require the SEDS-type PG synthase called RodA, whereas the other major class of PG synthases called class A penicillin-binding proteins (aPBPs) are not required for this mode of growth. Instead, they are thought to be important for maintaining the integrity of the PG matrix in organisms growing by dispersed elongation. In contrast, based on prior genetic studies in M. tuberculosis and related members of the Corynebacterineae suborder, the aPBPs are widely believed to be essential for polar growth, with RodA being dispensable. However, polar growth has not been directly assessed in mycobacterial or corynebacterial mutants lacking aPBP-type PG synthases. We therefore investigated the relative roles of aPBPs and RodA in polar growth using Corynebacterium glutamicum as a model member of Corynebacterineae. Notably, we discovered that the aPBPs are dispensable for polar growth and that this growth mode can be mediated by either an aPBP-type or a SEDS-type enzyme functioning as the sole elongation PG synthase. Thus, our results reveal that the mechanism of polar elongation is fundamentally flexible and, unlike dispersed elongation, can be effectively mediated in C. glutamicum by either a SEDS-bPBP or an aPBP-type synthase. IMPORTANCE The Corynebacterineae suborder includes a number of major bacterial pathogens. These organisms grow by polar extension unlike most well-studied model bacteria, which grow by inserting wall material at dispersed sites along their length. A better understanding of polar growth promises to uncover new avenues for targeting mycobacterial and corynebacterial infections. Here, we investigated the roles of the different classes of cell wall synthases for polar growth using Corynebacterium glutamicum as a model. We discovered that the polar growth mechanism is surprisingly flexible in this organism and, unlike dispersed synthesis, can function using either of the two known types of cell wall synthase enzymes.