Miracle-dz/UniFAR-FTUs huggingface dataset:
An Abnormal Tibial Position Is Associated With Alterations in the Meniscal Matrix: A 3-Year Longitudinal Study After Anterior Cruciate Ligament Reconstruction

Background: An altered tibial position is still present despite anterior cruciate ligament (ACL) reconstruction. It has been demonstrated that an abnormal tibial position after an ACL injury may play a role in subsequent injuries to the meniscus, which can lead to early cartilage degeneration. Purpose: To determine changes in both the tibial position and the meniscal matrix present before and after ACL reconstruction as well as to evaluate the association between these 2 variables in ACL-injured knees 3 years after reconstruction. Study Design: Cohort study; Level of evidence, 2. Methods: Bilateral knee magnetic resonance imaging (MRI) of 32 patients with unilateral ACL injuries was performed before reconstruction; 13 control participants also underwent MRI. Follow-up MRI was performed up to 3 years after surgery. Tibial position, internal tibial rotation, and T1ρ and T2 values of the menisci were calculated using an in-house MATLAB program. Student t tests and multiple linear regression were used to compare differences between injured, uninjured, and control knees as well as to assess correlations between the tibial position at 3 years and 3-year changes in quantitative MRI meniscal relaxation values. Results: The tibial position of injured knees was more anterior than that of uninjured knees at baseline, 6 months, and 1, 2, and 3 years (P < .05 for all). The T1ρ and T2 values of the menisci of injured knees were greater than those of uninjured and control knees in the posterior lateral and posterior medial horns up to 1 and 2 years after surgery, respectively (P < .05 for all). The tibial position at 3 years was associated with increased T2 values from baseline to 3 years in the posterior medial horn (β = 0.397; P = .031) and anterior medial horn (β = 0.360; P = .040). Conclusion: Results of the current study indicate that there is a persistently altered tibial position after ACL reconstruction. Initial preoperative meniscal abnormalities show prolonged but gradual improvement. Additionally, correlations between the tibial position and changes in the medial meniscal matrix suggest that the tibial position may play a role in the increased susceptibility to medial meniscal tears seen after reconstruction. The development of newer surgical techniques must address a persistently altered tibial position. Quantitative MRI is an effective instrument to evaluate meniscal matrix changes and can serve as an early radiological tool for meniscal injuries.
A Glucuronoxylomannan Epitope Exhibits Serotype-Specific Accessibility and Redistributes towards the Capsule Surface during Titanization of the Fungal Pathogen Cryptococcus neoformans

Disseminated infections with the fungal species Cryptococcus neoformans or, less frequently, Cryptococcus gattii are an important cause of mortality in immunocompromised individuals. Central to the virulence of both species is an elaborate polysaccharide capsule that consists predominantly of glucuronoxylomannan (GXM). ABSTRACT Disseminated infections with the fungal species Cryptococcus neoformans or, less frequently, Cryptococcus gattii are an important cause of mortality in immunocompromised individuals. Central to the virulence of both species is an elaborate polysaccharide capsule that consists predominantly of glucuronoxylomannan (GXM). Due to its abundance, GXM is an ideal target for host antibodies, and several monoclonal antibodies (mAbs) have previously been derived using purified GXM or whole capsular preparations as antigens. In addition to their application in the diagnosis of cryptococcosis, anti-GXM mAbs are invaluable tools for studying capsule structure. In this study, we report the production and characterization of a novel anti-GXM mAb, Crp127, that unexpectedly reveals a role for GXM remodeling during the process of fungal titanization. We show that Crp127 recognizes a GXM epitope in an O-acetylation-dependent, but xylosylation-independent, manner. The epitope is differentially expressed by the four main serotypes of Cryptococcus neoformans and C. gattii, is heterogeneously expressed within clonal populations of C. gattii serotype B strains, and is typically confined to the central region of the enlarged capsule. Uniquely, however, this epitope redistributes to the capsular surface in titan cells, a recently characterized morphotype where haploid 5-μm cells convert to highly polyploid cells of >10 μm with distinct but poorly understood capsular characteristics. Titan cells are produced in the host lung and critical for successful infection. Crp127 therefore advances our understanding of cryptococcal morphological change and may hold significant potential as a tool to differentially identify cryptococcal strains and subtypes.
Pain and affective distress in arthritis: relationship to immunity and inflammation

ABSTRACT Introduction: Most arthritides are associated with pain and psychological distress (clinically significant depression and anxiety). Pain and depression are mutually exacerbating; both may continue even when joint involvement appears well controlled. Area covered: There is strong evidence that arthritis-related stress impacts the central nervous system and, together with peripheral inflammatory changes, can cause central sensitization that can lead to chronic pain and worsening of affective distress. Cytokines and chemokines participate both in joint inflammation and in central sensitization. We review evidence of these relationships in five arthritides, namely rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, gout, and in osteoarthritis of the hips and knees. Central sensitization in these conditions results in long-lasting pain and psychological distress. Expert commentary: Chronic pain and depression are important but often neglected in the clinical assessment and treatment of arthritis. The potential role of biologic cytokines and Janus kinase inhibitors in dealing with these symptoms needs further study.
A retrospective study of mortality in Eurasian lynx (Lynx lynx) in UK zoos

IUCN currently classifies the Eurasian lynx (Lynx lynx) as “Least Concern,” however, across its six to nine subspecies, some isolated populations are classified as “Endangered” or “Critically Endangered. ” Despite this and the species’ relative ubiquity in European zoos, a retrospective mortality study of a captive population has not previously been performed. By analyzing necropsy reports, animal records, and the European studbook, we were able to ascertain a cause of death for 38 (73%) of the 52 recorded lynx deaths in UK zoos during the study period (January 1, 2000 to November 1, 2015). “Culling” as part of population management was the most common cause of death (21%) followed by neoplastic (16%), circulatory (11%), neurological (11%), and genitourinary (11%) disease. “Geriatric” individuals accounted for 62% of lynx to die within the study period, 23% were “neonates” and 15% “adults. ” Neoplasia, circulatory disease, and culling were the leading causes of death in each of these age categories, respectively. Excluding “culls” and “neonates,” the mean age at death was 18.81 ± 0.42 years, consistent with existing data. Squamous cell carcinoma was reported in three individuals (8%) and suspected idiopathic epilepsy in four individuals (11%), warranting further investigation. Intraspecific killing (3%) and neonatal mortality, excluding culls, (14%) were reported with lower prevalence than expected based on previous studies of similar species. The lack of data available and high incidence of culling of individuals with a high inbreeding coefficient highlights the need for improved record‐keeping and consultation with the studbook coordinator, respectively.
Kernel-Based Distance Metric Learning for Supervised $k$ -Means Clustering

Finding an appropriate distance metric that accurately reflects the (dis)similarity between examples is a key to the success of <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>-means clustering. While it is not always an easy task to specify a good distance metric, we can try to learn one based on prior knowledge from some available clustered data sets, an approach that is referred to as supervised clustering. In this paper, a kernel-based distance metric learning method is developed to improve the practical use of <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>-means clustering. Given the corresponding optimization problem, we derive a meaningful Lagrange dual formulation and introduce an efficient algorithm in order to reduce the training complexity. Our formulation is simple to implement, allowing a large-scale distance metric learning problem to be solved in a computationally tractable way. Experimental results show that the proposed method yields more robust and better performances on synthetic as well as real-world data sets compared to other state-of-the-art distance metric learning methods.
The effect of a lifestyle risk reduction intervention on lifestyle adherence and health‐related quality of life in nonsmall cell lung cancer survivors: Feasibility study outcomes

Phyllis F. Cantor Center for Research in Nursing and Patient Care Services, Dana‐Farber Cancer Institute, Boston, Massachusetts, USA Division of Biostatistics, Department of Data Sciences, Dana‐Farber Cancer Institute, Boston, Massachusetts, USA Division of Biostatistics, Department of Data Sciences (Dana-Farber Cancer Institute) and Department of Biostatistics, Harvard T.H. Chan School of Public Health, Dana‐Farber Cancer Institute, Boston, Massachusetts, USA College of Education, Health and Human Sciences, University of Tennesee, Knoxville, USA College of Nursing and Health Sciences, University of Massachusetts‐, Boston, Tennessee, USA Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, Massachusetts, USA Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
Electronic and optical characterization of 2D Ti2C and Nb2C (MXene) thin films

Two-dimensional (2D) transition metal carbides and/or nitrides (MXenes) are a new class of 2D materials, with extensive opportunities for property tailoring due to the numerous possibilities for varying chemistries and surface terminations. Here, Ti2AlC and Nb2AlC MAX phase epitaxial thin films were deposited on sapphire substrates by physical vapor deposition. The films were then etched in LiF/HCl solutions, yielding Li-intercalated, 2D Ti2CTz and Nb2CTz films, whose terminations, transport and optical properties were characterized. The former exhibits metallic conductivity, with weak localization below 50 K. In contrast, the Nb-based film exhibits an increase in resistivity with decreasing temperature from RT down to 40 K consistent with variable range hopping transport. The optical properties of both films were determined from spectroscopic ellipsometry in the 0.75 to 3.50 eV range. The results for Ti2CTz films confirm the metallic behavior. In contrast, no evidence of metallic behavior is observed for the Nb2CTz film. The present work therefore demonstrates that one fruitful approach to alter the electronic and optical properties of MXenes is to change the nature of the transition metal.
Interindividual and Regional Variability in Drug Transporter Abundance at the Human Blood–Brain Barrier Measured by Quantitative Targeted Proteomics

For in vitro to in vivo extrapolation (IVIVE) of brain distribution of drugs that are transported at the human blood–brain barrier (BBB), it is important to quantify the interindividual and regional variability of drug transporter abundance at this barrier. Therefore, using quantitative targeted proteomics, we compared the abundance of adenosine triphosphate–binding cassette and solute carrier transporters in brain microvascular endothelial cells (BMECs) isolated from postmortem specimens of two matched brain regions, the occipital (Brodmann Area (BA)17) and parietal (BA39) lobe, from 30 adults. Of the quantifiable transporters, the abundance ranked: glucose transporter (GLUT)1 > breast cancer resistance protein > P‐glycoprotein (P‐gp) > equilibrative nucleoside transporter (ENT)1 > organic anion‐transporting polypeptide (OATP)2B1. The abundance of multidrug resistance protein 1/2/3/4, OATP1A2, organic anion transporter (OAT)3, organic cation transporter (OCT)1/2, OCTN1/2, or ENT2 was below the limit of quantification. Transporter abundance per gram of tissue (scaled using GLUT1 abundance in BMEC vs. brain homogenate) in BA17 was 30–42% higher than BA39. The interindividual variability in transporter abundance (percentage of coefficient of variation (%CV)) was 35–57% (BA17) and 27–46% (BA39). These data can be used in proteomics‐informed bottom‐up IVIVE to predict human brain drug distribution.
Dosage-Related Prebiotic Effects of Inulin in Formula-Fed Infants

Purpose The aim of this study was to identify the minimally meaningful dosage of inulin leading to a prebiotic effect in Indonesian infants. Methods In a randomized controlled double-blinded, parallel, 3-arm intervention study, 164 healthy formula-fed infants aged 3 to 5 months first obtained formula-A (without inulin) during a 4-week adaptation period. Subsequently, 142 subjects were subjected to a 4-week feeding period by administering either formula-A (no inulin), formula-B (0.2 g/100 mL inulin) or formula-C (0.4 g/100 mL inulin). The primary outcome parameter was %-bifidobacteria in faecal samples determined using quantitative polymerase chain reaction analyses. Secondary outcome parameters were faecal %-lactobacilli, pH and stool frequency, and consistency. Growth and tolerance/adverse effects were recorded as safety parameters. Results Typical %-bifidobacteria and %-lactobacilli at the end of the adaptation period in the study population were 14% and 2%, respectively. For faecal pH, significant differences between formula groups A vs. C and A vs. B were found at the end of the intervention period. Testing for differences in faecal %-bifidobacteria and %-lactobacilli between groups was hampered by non-normal data set distributions; no statistically significant differences were obtained. Comparisons within groups revealed that only in formula group C, all the three relevant parameters exhibited a significant effect with an increase in faecal %-bifidobacteria and %-lactobacilli and a decrease in pH. Conclusion A consistent prebiotic effect along with a decrease in pH and increase in %-bifidobacteria and %-lactobacilli was found only in the group administered 0.4 g inulin/100 mL.
The impact of arterial hypertension on left ventricular strain in patients with aortic stenosis and preserved ejection fraction.

OBJECTIVE The influence of arterial hypertension on aortic stenosis severity is still controversial. The aim of this study was to evaluate the influence of hypertension on LV strain in patients with moderate and severe aortic stenosis. METHODS This cross-sectional study included 115 patients with moderate and severe aortic stenosis and preserved LV ejection fraction (>50%) and 89 age-matched normotensive and hypertensive controls who underwent comprehensive echocardiographic examination. Aortic stenosis patients were divided into normotensive and hypertensive groups. RESULTS There was no significant difference in LV ejection fraction between hypertensive and normotensive aortic stenosis patients. LV mass index gradually increased with the grade of aortic stenosis. LV global longitudinal strain, as well as endocardial and epicardial longitudinal strains, was significantly lower in hypertensive patients with severe aortic stenosis than in their normotensive counterparts. There was no significant difference in LV global circumferential strain between normotensive and hypertensive patients with severe aortic stenosis. Among patients with moderate aortic stenosis, there was no difference in global longitudinal strain between normotensives and hypertensive patients, whereas circumferential was significantly lower in hypertensive patients. LV radial strain was reduced in patients with severe aortic stenosis than in control subjects. SBP and mean aortic valve gradient were associated with LV global longitudinal and circumferential strains in aortic stenosis patients independently of LV mass index, LVEF, age and BMI. CONCLUSION Hypertension had additional significant negative influence on LV mechanics in patients with significant aortic stenosis. Blood pressure was associated with LV global longitudinal and circumferential strains in aortic stenosis patients independently of main clinical and demographic characteristics.
Targeting Bacillus cereus cells: increasing efficiency of antimicrobials by the bornylpossessing 2(5Н)-furanone derivative.

Among a variety of antimicrobial compounds, the derivatives of 2(5H)-furanone exhibit different effects on Firmicutes and Proteobacteria. While inhibiting quorum-dependent biofilm formation and virulence factor expression by Gram-negative bacteria through specific interference with the AI-2 signaling pathways, these compounds demonstrate bactericidal effects against Gram-positive bacteria. Here we report that 3,4-dichloro-5(S)-[(1S,2R,4S)-1,7,7-trimethylbicyclo[2.2. 1]heptan-2-yloxy]-2(5H)-furanone designed as F123 inhibits growth and biofilm formation by the food-poisoning bacterium Bacillus cereus at 8 μg/ ml and kills bacteria at 16 μg/ml. While the growth of Staphylococcus aureus, Staphylococcus epidermidis, Micrococcus luteus, Bacillus subtilis were also inhibited at 8-16 μg/ml of F123, no bactericidal effect on these strains was observed at concentrations up to 128 μg/ml, suggesting pronounced specificity of F123 for B. cereus. In a checker-board assay F123 increased the efficacy of amikacin, gentamicin and benzalkonium chloride against B. cereus with medians of fractional inhibitory concentration index of 0.38, 0.56 and 0.56, respectively. Moreover, the number of viable B. cereus cells in biofilm was reduced by more than 3 orders of magnitude at 64 μg/ml of F123, suggesting its chemotype as a promising enhancer for specific treatment of B. cereus-associated topical infections, including biofilm-embedded bacteria.
A Deep Neural Network-Based Pain Classifier Using a Photoplethysmography Signal

Side effects occur when excessive or low doses of analgesics are administered compared to the required amount to mediate the pain induced during surgery. It is important to accurately assess the pain level of the patient during surgery. We proposed a pain classifier based on a deep belief network (DBN) using photoplethysmography (PPG). Our DBN learned about a complex nonlinear relationship between extracted PPG features and pain status based on the numeric rating scale (NRS). A bagging ensemble model was used to improve classification performance. The DBN classifier showed better classification results than multilayer perceptron neural network (MLPNN) and support vector machine (SVM) models. In addition, the classification performance was improved when the selective bagging model was applied compared with the use of each single model classifier. The pain classifier based on DBN using a selective bagging model can be helpful in developing a pain classification system.
Auxin-Inducible Depletion of the Essentialome Suggests Inhibition of TORC1 by Auxins and Inhibition of Vrg4 by SDZ 90-215, a Natural Antifungal Cyclopeptide

Gene knockout and knockdown strategies have been immensely successful probes of gene function, but small molecule inhibitors (SMIs) of gene products allow much greater time resolution and are particularly useful when the targets are essential for cell replication or survival. SMIs also serve as lead compounds for drug discovery. However, discovery of selective SMIs is costly and inefficient. The action of SMIs can be modeled simply by tagging gene products with an auxin-inducible degron (AID) that triggers rapid ubiquitylation and proteasomal degradation of the tagged protein upon exposure of live cells to auxin. To determine if this approach is broadly effective, we AID-tagged over 750 essential proteins in Saccharomyces cerevisiae and observed growth inhibition by low concentrations of auxin in over 66% of cases. Polytopic transmembrane proteins in the plasma membrane, Golgi complex, and endoplasmic reticulum were efficiently depleted if the AID-tag was exposed to cytoplasmic OsTIR1 ubiquitin ligase. The auxin analog 1-napthylacetic acid (NAA) was as potent as auxin on AID-tags, but surprisingly NAA was more potent than auxin at inhibiting target of rapamycin complex 1 (TORC1) function. Auxin also synergized with known SMIs when acting on the same essential protein, indicating that AID-tagged strains can be useful for SMI screening. Auxin synergy, resistance mutations, and cellular assays together suggest the essential GMP/GDP-mannose exchanger in the Golgi complex (Vrg4) as the target of a natural cyclic peptide of unknown function (SDZ 90-215). These findings indicate that AID-tagging can efficiently model the action of SMIs before they are discovered and can facilitate SMI discovery.
Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)

Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.
Posttraumatic stress disorder symptoms and mindfulness facets in relation to suicide risk among firefighters.

OBJECTIVE Posttraumatic stress disorder (PTSD) symptoms are associated with increased suicide risk among firefighters. Few studies have examined modifiable factors, such as mindfulness facets, that might attenuate this association. This study examined the interactive effects of PTSD symptoms and mindfulness facets in relation to suicide risk among firefighters. METHOD Overall, 831 career firefighters were assessed for PTSD symptoms, mindfulness facets, and suicide risk via the PTSD Checklist for DSM-5, Five Facet Mindfulness Questionnaire, and Suicidal Behaviors Questionnaire-Revised, respectively. RESULTS Greater PTSD symptoms were associated with more severe suicide risk; however, higher levels of two specific mindfulness facets, acting with awareness and nonjudging of inner experience, attenuated this association. By contrast, higher levels of the observing facet of mindfulness potentiated the association between PTSD symptoms and suicide risk. CONCLUSIONS Suicide prevention initiatives among firefighters, particularly those experiencing trauma-related sequelae, might benefit from the inclusion of mindfulness-based practices alongside frontline empirically-supported approaches.