Miracle-dz/UniFAR-FTUs huggingface dataset:
Air pollution induces Staphylococcus aureus USA300 respiratory tract colonization mediated by specific bacterial genetic responses involving the global virulence gene regulators Agr and Sae

Summary Exposure to particulate matter (PM), a major component of air pollution, is associated with exacerbation of chronic respiratory disease, and infectious diseases such as community‐acquired pneumonia. Although PM can cause adverse health effects through direct damage to host cells, our previous study showed that PM can also impact bacterial behaviour by promoting in vivo colonization. In this study we describe the genetic mechanisms involved in the bacterial response to exposure to black carbon (BC), a constituent of PM found in most sources of air pollution. We show that Staphylococcus aureus strain USA300 LAC grown in BC prior to inoculation showed increased murine respiratory tract colonization and pulmonary invasion in vivo, as well as adhesion and invasion of human epithelial cells in vitro. Global transcriptional analysis showed that BC has a widespread effect on S. aureus transcriptional responses, altering the regulation of the major virulence gene regulators Sae and Agr and causing increased expression of genes encoding toxins, proteases and immune evasion factors. Together these data describe a previously unrecognized causative mechanism of air pollution‐associated infection, in that exposure to BC can increase bacterial colonization and virulence factor expression by acting directly on the bacterium rather than via the host.
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning

Abstract Recent advances in machine learning and natural language processing have made it possible to profoundly advance our ability to accurately predict protein structures and their functions. While such improvements are significantly impacting the fields of biology and biotechnology at large, such methods have the downside of high demands in terms of computing power and runtime, hampering their applicability to large datasets. Here, we present NetSurfP-3.0, a tool for predicting solvent accessibility, secondary structure, structural disorder and backbone dihedral angles for each residue of an amino acid sequence. This NetSurfP update exploits recent advances in pre-trained protein language models to drastically improve the runtime of its predecessor by two orders of magnitude, while displaying similar prediction performance. We assessed the accuracy of NetSurfP-3.0 on several independent test datasets and found it to consistently produce state-of-the-art predictions for each of its output features, with a runtime that is up to to 600 times faster than the most commonly available methods performing the same tasks. The tool is freely available as a web server with a user-friendly interface to navigate the results, as well as a standalone downloadable package.
Returning to Activity After Anterior Cruciate Ligament Revision Surgery: An Analysis of the Multicenter Anterior Cruciate Ligament Revision Study (MARS) Cohort at 2 Years Postoperative

Background: Patients with anterior cruciate ligament (ACL) revision report lower outcome scores on validated knee questionnaires postoperatively compared to cohorts with primary ACL reconstruction. In a previously active population, it is unclear if patient-reported outcomes (PROs) are associated with a return to activity (RTA) or vary by sports participation level (higher level vs. recreational athletes). Hypotheses: Individual RTA would be associated with improved outcomes (ie, decreased knee symptoms, pain, function) as measured using validated PROs. Recreational participants would report lower PROs compared with higher level athletes and be less likely to RTA. Study Design: Cohort study; Level of evidence, 2. Methods: There were 862 patients who underwent a revision ACL reconstruction (rACLR) and self-reported physical activity at any level preoperatively. Those who did not RTA reported no activity 2 years after revision. Baseline data included patient characteristics, surgical history and characteristics, and PROs: International Knee Documentation Committee questionnaire, Marx Activity Rating Scale, Knee injury and Osteoarthritis Outcome Score, and the Western Ontario and McMaster Universities Osteoarthritis Index. A binary indicator was used to identify patients with same/better PROs versus worse outcomes compared with baseline, quantifying the magnitude of change in each direction, respectively. Multivariable regression models were used to evaluate risk factors for not returning to activity, the association of 2-year PROs after rACLR surgery by RTA status, and whether each PRO and RTA status differed by participation level. Results: At 2 years postoperatively, approximately 15% did not RTA, with current smokers (adjusted odds ratio [aOR] = 3.3; P = .001), female patients (aOR = 2.9; P < .001), recreational participants (aOR = 2.0; P = .016), and those with a previous medial meniscal excision (aOR = 1.9; P = .013) having higher odds of not returning. In multivariate models, not returning to activity was significantly associated with having worse PROs at 2 years; however, no clinically meaningful differences in PROs at 2 years were seen between participation levels. Conclusion: Recreational-level participants were twice as likely to not RTA compared with those participating at higher levels. Within a previously active cohort, no RTA was a significant predictor of lower PROs after rACLR. However, among patients who did RTA after rACLR, approximately 20% reported lower outcome scores. Most patients with rACLR who were active at baseline improved over time; however, patients who reported worse outcomes at 2 years had a clinically meaningful decline across all PROs.
Identification of seasonal variation in the diagnosis of acute myeloid leukaemia: a population‐based study

Until now, the role that seasonal factors play in the aetiology of acute myeloid leukaemia (AML) has been unclear. Demonstration of seasonality in AML diagnosis would provide supportive evidence of an underlying seasonal aetiology. To investigate the potential seasonal and long‐term trends in AML diagnosis in an overall population and in subgroups according to sex and age, we used population‐based data from a Spanish hospital discharge registry. We conducted a larger study than any to date of 26 472 cases of AML diagnosed in Spain between 2004 and 2015. Using multivariable Poisson generalized linear autoregressive moving average modelling, we found an upward long‐term trend, with monthly incidence rates of AML annually increasing by 0.4% [95% confidence interval (CI), 0.2%–0.6%; p = 0.0011]. January displayed the highest incidence rate of AML, with a minimum average difference of 7% when compared to February (95% CI, 2%–12%; p = 0.0143) and a maximum average difference of 16% compared to November (95% CI, 11%–21%; p < 0.0001) and August (95% CI, 10%–21%; p < 0.0001). Such seasonal effect was consistent among subgroups according to sex and age. Our finding that AML diagnosis is seasonal strongly implies that seasonal factors, such as infectious agents or environmental triggers, influence the development and/or proliferation of disease, pointing to prevention opportunities.
A whiff of the future: functions of phenylalanine‐derived aroma compounds and advances in their industrial production

Summary Plants produce myriad aroma compounds—odorous molecules that are key factors in countless aspects of the plant's life cycle, including pollinator attraction and communication within and between plants. For humans, aroma compounds convey accurate information on food type, and are vital for assessing the environment. The phenylpropanoid pathway is the origin of notable aroma compounds, such as raspberry ketone and vanillin. In the last decade, great strides have been made in elucidating this pathway with the identification of numerous aroma‐related biosynthetic enzymes and factors regulating metabolic shunts. These scientific achievements, together with public acknowledgment of aroma compounds' medicinal benefits and growing consumer demand for natural products, are driving the development of novel biological sources for wide‐scale, eco‐friendly, and inexpensive production. Microbes and plants that are readily amenable to metabolic engineering are garnering attention as suitable platforms for achieving this goal. In this review, we discuss the importance of aroma compounds from the perspectives of humans, pollinators and plant–plant interactions. Focusing on vanillin and raspberry ketone, which are of high interest to the industry, we present key knowledge on the biosynthesis and regulation of phenylalanine‐derived aroma compounds, describe advances in the adoption of microbes and plants as platforms for their production, and propose routes for improvement.
The distribution of phenotypic and genotypic characters within streptomycetes and their relationship to antibiotic production

A collection of over 300 streptomycetes, comprising both natural isolates and type strains, were assessed for the distribution of fatty acids, antibiotic resistances, compounds in solvent extracts, and sequences that hybridized to antibiotic resistance gene probes. These data were clustered using numerical methods and groups of similar strains were delimited. The production of selected antibiotics by all strains was also determined and the data examined for any correlations with the defined clusters. Production of bioactive compounds was observed in twenty percent of the natural isolates studied; nigericin and geldanamycin production was common. Geldanamycin was only biosynthesized by strains which also produced nigericin and most strains which were thought to produce a novel antibiotic were also capable of nigericin production. When the sources and concentrations of nutrients in the cultures of antibiotic producers were altered, differentiation responses and the expression of antibiotic production were found to be strain specific. In addition to this, nigericin production could be repressed by oxygen limitation. In a production medium, fluctuations in fatty acid profiles occurred concomitantly with antibiotic biosynthesis, although this could not be correlated. However, fatty acid profiles did not allow the delimitation of groups of taxonomically related strains, which were cultured in a growth medium. Thin layer chromatography patterns obtained from the solvent extracts of streptomycete cultures showed much variation and were not suitable for use as systematic data. Antibiotic resistance patterns allowed the delimitation of bioactive strains from certain non-bioactive groups of strains; antibiotic producers showed multiple antibiotic resistance phenotypes, whereas a single selected resistance and a multiple sensitive phenotype was characteristic of non-bioactive strains. Most strains were resistant to penicillin and a large proportion were resistant to nigericin, but strains with resistance to aminoglycosides were rare. Preliminary evidence showed that DNA from strains with multiple resistance patterns hybridized more often to gene probes (these were internal fragments of aphD, aph, vph, bar, tsr Nbr) than did DNA from strains with multiple sensitive phenotypes. Similarites were observed between strains grouped by their hybridization patterns and those grouped by the chemical class of their product. This work also allowed the selection of phenotypically resistant strains with different resistance genes and possible resistance mechanisms.
A Dynamic Threshold Approach for Tarnished Plant Bug (Hemiptera: Miridae) Management in the Midsouthern U.S. Cotton

Abstract One of the most economically important pests of cotton, Gossypium hirsutum L. , in the midsouth region of the United States is the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois, Hemiptera: Miridae). Tarnished plant bug populations across the region have exhibited widespread resistance to numerous insecticide classes. To minimize late season resistance development, reducing unwarranted applications during the late flowering period can aid in resistance management and potentially reduce input costs. Trials were conducted during 2019 and 2020 to evaluate the impacts of tarnished plant bug populations in the later flowering period of cotton by modifying or terminating threshold regimes during the later weeks of bloom. Results showed that dynamic thresholds altered at the fourth week of bloom or later can reduce the number of late season applications made with no penalty to yield. Additionally, when utilizing a week of bloom termination approach, no significant yield losses were seen when terminating applications after the fourth week of bloom. These data may offer an alternative method to managing tarnished plant bug populations during the later flowering period of midsouth cotton.
Primary characteristics and outcomes of newly diagnosed low-grade endometrial stromal sarcoma

Objective To assess potential predictive variables for nodal metastasis and survival outcomes in patients with newly diagnosed, low-grade endometrial stromal sarcoma. Methods We performed a single-institution, retrospective analysis of consecutive patients with newly diagnosed, low-grade endometrial stromal sarcoma who presented between January 1, 1980 and December 31, 2019 and underwent hysterectomy at our institution or presented within 3 months of primary surgery elsewhere before recurrence. Patients who presented to our institution only at recurrence were excluded. Patients with <3 months of follow-up were excluded from survival analyses. Results We identified 127 consecutive patients for analysis. Median age at diagnosis was 48 years (range 19–88 years); 91 (74.6%) of 127 were pre-menopausal; and 74 (58.3%) of 127 had uterine-confined, stage I tumors. Of 56 patients (44.1%) who underwent lymph node sampling, 10 (17.9%) had nodal metastasis. Of the 10 with nodal metastasis, 1 (10%) did not have lymphadenopathy or extra-uterine disease, 4 (40%) had lymphadenopathy only, 1 (10%) had extra-uterine disease only, and 4 (40%) had both. Among the 29 patients without apparent extra-uterine disease or gross lymphadenopathy, there was one occult lymph node metastasis (3.4%). Gross lymphadenopathy at time of surgery was predictive for lymph node metastasis (p<0.001). Median follow-up was 69 months (range 4–336) for the 95 patients included in the survival analyses. The 5-year progression-free survival and disease-specific survival rates were 79.8% and 90.8%, respectively. Patients with stage I tumors had longer progression-free survival than those with stage II–IV disease (p<0.001); there was no difference in disease-specific survival (p=0.63). Post-operative observation versus adjuvant therapy with hormone blockade or radiation therapy did not result in progression-free survival differences for stage I or completely resected stage II–IV disease (p=0.50 and p=0.81, respectively). Similarly, there was no disease-specific survival difference for completely resected stage II–IV disease (p=0.3). Conclusions Lymph node dissection in patients with low-grade endometrial stromal sarcoma should be reserved for those with clinically suspicious lymphadenopathy. Disease stage correlated with progression-free survival but not disease-specific survival. Post-operative therapy did not improve progression-free survival or disease-specific survival.
Racial and ethnic and income disparities in COVID‐19 vaccination among Medicare beneficiaries

Older adults have been disproportionately affected by the COVID‐19 pandemic. Despite the widespread availability and proved effectiveness of COVID‐19 vaccines, the issue of inequity in vaccine uptake in the United States is a potential concern among different populations. This study examined racial and ethnic and income disparities in COVID‐19 vaccination rate among Medicare beneficiaries.
Cardiopulmonary exercise testing and efficacy of percutaneous coronary intervention: a substudy of the ORBITA trial

Abstract Aims Oxygen-pulse morphology and gas exchange analysis measured during cardiopulmonary exercise testing (CPET) has been associated with myocardial ischaemia. The aim of this analysis was to examine the relationship between CPET parameters, myocardial ischaemia and anginal symptoms in patients with chronic coronary syndrome and to determine the ability of these parameters to predict the placebo-controlled response to percutaneous coronary intervention (PCI). Methods and results Patients with severe single-vessel coronary artery disease (CAD) were randomized 1:1 to PCI or placebo in the ORBITA trial. Subjects underwent pre-randomization treadmill CPET, dobutamine stress echocardiography (DSE) and symptom assessment. These assessments were repeated at the end of a 6-week blinded follow-up period. A total of 195 patients with CPET data were randomized (102 PCI, 93 placebo). Patients in whom an oxygen-pulse plateau was observed during CPET had higher (more ischaemic) DSE score [+0.82 segments; 95% confidence interval (CI): 0.40 to 1.25, P = 0.0068] and lower fractional flow reserve (−0.07; 95% CI: −0.12 to −0.02, P = 0.011) compared with those without. At lower (more abnormal) oxygen-pulse slopes, there was a larger improvement of the placebo-controlled effect of PCI on DSE score [oxygen-pulse plateau presence (Pinteraction = 0.026) and oxygen-pulse gradient (Pinteraction = 0.023)] and Seattle angina physical-limitation score [oxygen-pulse plateau presence (Pinteraction = 0.037)]. Impaired peak VO2, VE/VCO2 slope, peak oxygen-pulse, and oxygen uptake efficacy slope was significantly associated with higher symptom burden but did not relate to severity of ischaemia or predict response to PCI. Conclusion Although selected CPET parameters relate to severity of angina symptoms and quality of life, only an oxygen-pulse plateau detects the severity of myocardial ischaemia and predicts the placebo-controlled efficacy of PCI in patients with single-vessel CAD.
Ozone Therapy for Dermatological Conditions: A Systematic Review.

Background Known in the past for its toxic aspect as the main urban pollutant, in the last few decades, ozone has been gaining greater visibility for its possible antimicrobial, antiviral, and antioxidant effects when used in human dermatological pathologies. Despite the reports of clinical benefits, the standard dosage for clinical efficacy and safety are yet not clear, nor are its means of application and its true acting mechanism. Objective We conducted a review to determine the efficacy and safety of ozone therapy for a variety of dermatological conditions. Methods We considered clinical trials (both randomized and non-randomized) published between December 2020 and March 2021 as long as they provided some PICO information, i.e., population (P), intervention (I), and study design. The skin dermatological conditions researched were: acne, dermatitis, psoriasis, systemic sclerosis, herpes, aging, ulcers, and skin scarring. Results A total of 326 articles were identified and 150 remained after duplicates were removed. After titles, abstracts and full articles were read, 17 articles were included in the systematic review (with 643 patients). Conclusion Ozone therapy seems promising for some dermatological conditions; however, the articles included in this review had methodological limitations and did not sufficiently demonstrate sound evidence for safe therapy. Therefore, more studies with better methodological standards and longer-term assessments of side effects should be conducted to achieve better standards and safety in ozone therapy for dermatological conditions.
A Questionnaire Survey of German Thyroidologists on the Use of Thyroid Hormones in Hypothyroid and Euthyroid Patients: The THESIS (Treatment of Hypothyroidism in Europe by Specialists: An International Survey) Collaborative.

OBJECTIVE To identify the attitudes of German thyroid specialists towards the clinical treatment of hypothyroidism using thyroid hormones (TH). METHODS All members of the thyroid section of the German Endocrine Society (DGE) were e-mailed an invitation to participate in a web-based survey about substitution with TH. RESULTS Out of 206 members of the DGE's thyroid section, 163 (79.1%) responses were received and included in the analysis. Of responding members, 98.6% used levothyroxine (LT4) as the treatment of choice, and 45.4% also prescribed combination therapy with liothyronine (LT4+LT3) in their clinical practice (p<0.001). LT4+LT3 combination was favored in patients with persistent hypothyroidism symptoms despite biochemical euthyroidism on LT4 treatment (p<0.001). Of all respondents, 26.4% never indicated TH therapy for euthyroid patients (p<0.001), while the remainder would consider THs for one or more indications (62.9% for euthyroid infertile women with high anti-thyroid antibody levels (p<0.001), 7.1% in patients with severe hypercholesterolemia, as complementary treatment (p=0.007), and 57.1% in patients with simple goiter (p<0.001)). In conditions that could interfere with LT4 absorption, most respondents still preferred tablets and did not expect a significant difference when switching from one LT4 formulation to another. CONCLUSION For German thyroid specialists, LT4 is the treatment of choice for hypothyroidism. Combination therapy with LT4+LT3 was considered for patients with persistent symptoms. Even in conditions that could affect bioavailability, German thyroid specialists prefer LT4 tablets rather than other LT4 formulations, such as liquid or soft-gel capsules. The widespread use of thyroid hormone for non-hypothyroid conditions is not consistent with current evidence and needs further study.
The effect of duloxetine on mechanistic pain profiles, cognitive factors and clinical pain in patients with painful knee osteoarthritis—A randomized, double‐blind, placebo‐controlled, crossover study

Duloxetine is indicated in the management of pain in osteoarthritis. Evidence suggests that duloxetine modulates central pain mechanisms and cognitive factors, and these factors are assumed contributing to the analgesic effect. This proof‐of‐mechanism, randomized, placebo‐controlled, crossover, double‐blinded trial evaluated the effect of duloxetine on quantitative sensory testing (QST), cognitive factors and clinical pain in patients with osteoarthritis and to predict the analgesic effect.
Improving Fat Transplantation Survival and Vascularization with Adenovirus E4+ Endothelial Cell-Assisted Lipotransfer

Autologous fat transplantation is plagued by an unpredictable and often significant degree of graft loss. AdE4+ endothelial cells (ECs) are human endothelial cells that have been transduced with the E4ORF1 region of human adenovirus type 5, resulting in long-term preservation of EC proliferation and angiogenic capability without immortalization. We hypothesized that AdE4+ EC-enriched fat grafts would demonstrate improved volume retention secondary to enhanced angiogenesis. Three experimental groups were prepared by admixing 400 µL of patient lipoaspirate with 100 µL of AdE4+ EC suspensions (high AdE4+ EC concentration-enriched [5 × 106/mL], low AdE4+ EC concentration-enriched [1.25 × 106/mL], or PBS) and injected subcutaneously into the bilateral dorsa of nude mice. Fat transplants were explanted at 90 and 180 days for volumetric and histologic analyses. After both 90 and 180 days, AdE4+ EC-enriched fat grafts showed greater mean volume preservation compared to control grafts (p < 0.05). Regions of focal necrosis were only noticed in low AdE4+ EC concentration-enriched and control groups after 180 days. Histologic analysis demonstrated the presence of healthy adipocytes in all AdE4+ EC-enriched fat grafts in which both human and host ECs were evident after 90 and 180 days. AdE4+ EC enrichment improved fat graft volume preservation and vascularization in this murine xenograft model. Though further study is warranted, AdE4+ ECs demonstrated to be promising as a potential off-the-shelf adjunct for improving the volume, quality, and consistency of fat engraftment.