Miracle-dz/UniFAR-FTUs huggingface dataset:
Incidence and natural course of CT-detected pulmonary ground-glass nodules in Chinese women with breast cancer: a retrospective, single-center, long-term follow-up study in 4682 consecutive patients

Background Increased use of thin-section computed tomography (CT) scans has revealed that small lung nodules, termed ground-glass nodules, are frequent in primary breast cancer patients and are associated with pre-invasive or invasive pulmonary adenocarcinomas. However, little is known of the incidence and fate of ground-glass nodules. Purpose To elucidate the incidence and natural course of CT-detected pulmonary ground-glass nodules in Chinese women with breast cancer. Material and Methods We retrospectively reviewed data from female breast cancer patients who underwent lung CT scans and who were followed for ≥3 months after the initial scan to identify the incidence of ground-glass nodules and any changes in them during the follow-up period. Results Between January 2008 and April 2018, 693 out of 4682 breast cancer patients (14.8%) had persistent lung ground-glass nodules as detected by CT scan. The median age was 52 years (interquartile range [IQR] = 45–62 years). Median nodule size was 4.9 mm in diameter on initial CT scan. Frequency of growth was 7.5% (52/693 patients). Median volume doubling time was 1092 days (IQR = 719–1808 days) for 39 growing in size nodules. Initial nodule size, nodule type, and follow-up period were independent predictors of nodule growth. Conclusion Most pulmonary ground-glass nodules in breast cancer patients were stable during long-term follow-up; most growing nodules had an indolent clinical course, suggesting that nodules should be monitored until growth is detected. This information is clinically relevant for accurate diagnosis of cancer stage and for appropriate treatment plans for patients with lung ground-glass nodules.
Association of Epstein-Barr virus serological reactivation with transitioning to systemic lupus erythematosus in at risk individuals

Objective Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with unknown aetiology. Epstein-Barr virus (EBV) is an environmental factor associated with SLE. EBV maintains latency in B cells with frequent reactivation measured by antibodies against viral capsid antigen (VCA) and early antigen (EA). In this study, we determined whether EBV reactivation and single nucleotide polymorphisms (SNPs) in EBV-associated host genes are associated with SLE transition. Methods SLE patient relatives (n=436) who did not have SLE at baseline were recontacted after 6.3 (±3.9) years and evaluated for interim transitioning to SLE (≥4 cumulative American College of Rheumatology criteria); 56 (13%) transitioned to SLE prior to the follow-up visit. At both visits, detailed demographic, environmental, clinical information and blood samples were obtained. Antibodies against viral antigens were measured by ELISA. SNPs in IL10, CR2, TNFAIP3 and CD40 genes were typed by ImmunoChip. Generalised estimating equations were used to test associations between viral antibody levels and transitioning to SLE. Results Mean baseline VCA IgG (4.879±1.797 vs 3.866±1.795, p=0.0003) and EA IgG (1.192±1.113 vs 0.7774±0.8484, p=0.0236) levels were higher in transitioned compared with autoantibody negative non-transitioned relatives. Increased VCA IgG and EA IgG were associated with transitioning to SLE (OR 1.28 95% CI 1.07 to 1.53, p=0.007, OR 1.43 95% CI 1.06 to 1.93, p=0.02, respectively). Significant interactions were observed between CD40 variant rs48100485 and VCA IgG levels and IL10 variant rs3024493 and VCA IgA levels in transitioning to SLE. Conclusion Heightened serologic reactivation of EBV increases the probability of transitioning to SLE in unaffected SLE relatives.
Factors that Promote Resilience in Homeless Children and Adolescents in Ghana: A Qualitative Study

Several studies conducted on street youth have focused on causes of homelessness, their engagement in risky sexual behaviours and the prevalence of STIs, including HIV/AIDS. Although homeless youth are considered resilient, sparse literature exists on factors that promote resilience in this vulnerable group. Using a qualitative approach, semi-structured interviews were conducted with 16 purposively selected homeless children and youth (with a mean age of 14 years) from the Central Business District of Accra, Ghana. Thematic analysis was used to analyse the data. Findings showed that a strong religious belief, sense of humour, engagement in meaningful social interactive activities, reciprocal friendship, adherence to cultural norms and support from community-based organizations were identified as factors that help homeless youth cope with the multiple challenges of street life. Strengthening such protective factors could help ameliorate the impact of adverse conditions of these street youth.
First‐in‐man fully leadless transvenous CRT‐P with a transseptal implant of WISE‐CRT® system and Micra® PM

We describe the world's first fully leadless cardiac resynchronization therapy pacing implant with transseptal approach, in a patient with pacemaker dependency, atrial fibrillation, ischemic hypokinetic cardiomyopathy, and a history of pocket infections. After lead extraction, we implanted a MicraTranscathether Pacing System® (Medtronic, Minneapolis, MN, USA) as the sole right ventricular pacemaker, and the WISECRT system (EBR Systems, Sunnyvale, CA, USA) to provide biventricular pacing. We performed the WISECRT implant procedure using the transseptal approach given the presence of a prosthetic aortic mechanical valve, achieving satisfactory periprocedural results.
A PAK5–DNPEP–USP4 axis dictates breast cancer growth and metastasis

Although clinically associated with the progression of multiple cancers, the biological function of p21‐activated kinase 5 (PAK5) in breast cancer remains largely unknown. Here, we reveal that the PAK5–aspartyl aminopeptidase (DNPEP)–ubiquitin‐specific protease 4 (USP4) axis is involved in breast cancer progression. We show that PAK5 interacts with and phosphorylates DNPEP at serine 119. Functionally, we demonstrate that DNPEP overexpression suppresses breast cancer cell proliferation and invasion and restricts breast cancer growth and metastasis in mice. Furthermore, we identify USP4 as a downstream target of the PAK5–DNPEP pathway; DNPEP mediates USP4 downregulation. Importantly, we verify that DNPEP expression is frequently downregulated in breast cancer tissues and is negatively correlated with PAK5 and USP4 expression. PAK5 decreases DNPEP abundance via the ubiquitin–proteasome pathway. Consistently, analyses of clinical breast cancer specimens revealed significantly increased PAK5 and USP4 levels and an association between higher PAK5 and USP4 expression and worse breast cancer patient survival. These findings suggest a pivotal role for PAK5‐elicited signaling in breast cancer progression.
Molecular and Morphological Changes Induced by Leonardite-based Biostimulant in Beta vulgaris L.

Humic substances extracted from leonardite are widely considered to be bioactive compounds, influencing the whole-plant physiology and the crop yield. The aim of this work was to evaluate the effect of a new formulate based on leonardite in the early stage of growth of sugar beet (Beta vulgaris L.). A commercial preparation of leonardite (BLACKJAK) was characterized by ionomic analysis, solid-state 13C MAS NMR spectroscopy. Seedlings of sugar beet were grown in Hoagland’s solution under controlled conditions. After five days of growth, an aliquot of the concentrated BLACKJAK was added to the solution to obtain a final dilution of 1:1000 (0.5 mg C L−1). The sugar beet response in the early stage of growth was determined by evaluating root morphological traits as well as the changes in the expression of 53 genes related to key morphophysiological processes. Root morphological traits, such as total root length, fine root length (average diameter < 0.5 mm), and number of root tips, were significantly (p < 0.001) increased in plants treated with BLACKJAK, compared to the untreated plants at all sampling times. At the molecular level, BLACKJAK treatment upregulated many of the evaluated genes. Moreover, both Real Time PCR and digital PCR showed that genes involved in hormonal response, such as PIN, ARF3, LOGL 10, GID1, and BRI1, were significantly (p < 0.05) upregulated by treatment with BLACKJAK. Our study provides essential information to understand the effect of a leonardite-based formulate on plant growth hormone metabolism, although the molecular and physiological basis for these complicated regulatory mechanisms deserve further investigations.
Hafting of Middle Paleolithic tools in Latium (central Italy): New data from Fossellone and Sant’Agostino caves

Hafting of stone tools was an important advance in the technology of the Paleolithic. Evidence of hafting in the Middle Paleolithic is growing and is not limited to points hafted on spears for thrusting or throwing. This article describes the identification of adhesive used for hafting on a variety of stone tools from two Middle Paleolithic caves in Latium, Fossellone Cave and Sant’Agostino Cave. Analysis of the organic residue by gas chromatography/mass spectrometry shows that a conifer resin adhesive was used, in one case mixed with beeswax. Contrary to previous suggestions that the small Middle Paleolithic tools of Latium could be used by hand and that hafting was not needed since it did not improve their functionality, our evidence shows that hafting was used by Neandertals in central Italy. Ethnographic evidence indicates that resin, which dries when exposed to air, is generally warmed by exposure to a small fire thus softened to be molded and pushed in position in the haft. The use of resin at both sites suggests regular fire use, as confirmed by moderate frequencies of burnt lithics in both assemblages. Lithic analysis shows that hafting was applied to a variety of artifacts, irrespective of type, size and technology. Prior to our study evidence of hafting in the Middle Paleolithic of Italy was limited to one case only.
Elevated levels of eEF1A2 protein expression in triple negative breast cancer relate with poor prognosis

Eukaryotic elongation factor 1 alpha 2 (eEF1A2) is a translation factor selectively expressed by heart, skeletal muscle, nervous system and some specialized cells. Its ectopic expression relates with tumorigenesis in several types of human cancer. No data are available about the role of eEF1A2 in Triple Negative Breast Cancers (TNBC). This study investigated the relation between eEF1A2 protein levels and the prognosis of TNBC. A total of 84 TNBC diagnosed in the period 2002–2011 were included in the study. eEF1A2 protein level was measured in formalin-fixed paraffin-embedded tissues by immunohistochemistry in a semi-quantitative manner (sum of the percentage of positive cells x staining intensity) on a scale from 0 to 300. Cox regression assessed the association between eEF1A2 levels and disease-free survival (DFS) and breast cancer-specific survival (BCSS). Elevated values of eEF1A2 were associated with older age at diagnosis (p = 0.003), and androgen receptors positivity (p = 0.002). At univariate Cox analysis, eEF1A2 levels were not significantly associated with DFS and BCSS (p = 0.11 and p = 0.08, respectively) whereas adjusting for stage of disease, elevated levels of eEF1A2 protein resulted associated with poor prognosis (HR = 1.05, 95% CI: 1.01–1.11, p = 0.04 and HR = 1.07, 95% CI: 1.01–1.14, p = 0.03 for DFS and BCSS, respectively). This trend was confirmed analyzing negative versus positive samples by using categorized scores. Our data showed a negative prognostic role of eEF1A2 protein in TNBC, sustaining further investigations to confirm this result by wider and independent cohorts of patients.
A colonized general practice? A critical habermasian analysis of how general practitioners experience defensive medicine in their everyday working life

The aim of this article is to show how Jürgen Habermas’ communicative action theory serves as a useful tool in analysing and interpreting empirical data on how Danish general practitioners experience defensive medicine in their everyday working life. Through six qualitative focus group interviews with a total of 28 general practitioners (14 men and 14 women), the general practitioners’ understandings of and experiences with defensive medicine were unfolded and discussed. Traditionally, defensive medicine is understood as physicians’ deviation from sound medical practice due to fears of liability claims or lawsuits. In this study, however, a broader understanding of defensive medicine emerged as unnecessary medical actions that are more substantiated by feelings of demands and pressures than meaningful clinical behaviour. As a first analytical step, the data are contextualized drawing on the medical sociological literature that has theorized recent changes within primary health care such as regulation, audit, standardization and consumerism. Using Habermas’ theorization to further interpret the general practitioners’ experiences, we argue that central areas of the general practitioners’ clinical everyday work life can be seen as having become subject to the habermasian social and political processes of ‘strategic action’ and ‘colonization’. It is furthermore shown that the general practitioners share an impulse to resist these colonizing processes, hereby pointing to a need for challenging the increasingly defensive medical culture that seems to pervade the organization of general practice today.
On enhancing GridFTP and GPFS performances

One of the most demanding tasks which Computing in High Energy Physics has to deal with is reliable and high throughput transfer of large data volumes. Maximization and optimization of the data throughput are therefore key issues which have to be addressed by detailed investigations of the involved infrastructures and services. In this note, we present some transfer performance tests carried out at the INFN-CNAF Tier-1 center, using SLC4 64-bit Grid File Transfer Protocol (GridFTP) servers and a disk storage system based on the General Parallel File System (GPFS) from IBM. We describe the testbed setup and report the measurements of throughput performances in function of some fundamental variables, such as number of parallel file and number of streams per transfer, concurrent read and write activity and size of data blocks transferred. During this activity, we have verified that a significant improvement in performances of the GridFTP server can be obtained using 64bit version of Operating System and GPFS from IBM.
Use of prescription opioids among patients with rheumatic diseases compared to patients with hypertension in the USA: a retrospective cohort study

Objective Long-term opioid prescribing has increased amid concerns over effectiveness and safety of its use. We examined long-term prescription opioid use among patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), psoriatic arthritis (PsA) and ankylosing spondylitis (AS), compared with patients with hypertension (HTN). Methods We used Truven MarketScan, a US commercial claims database (2003–2014) and identified RA, SLE, PsA and AS cohorts, each matched by age and sex to patients with HTN. We compared long-term opioid prescription use during 1 year of follow-up and used multivariable Poisson regression model to estimate the relative risk (RR) of receiving opioid prescriptions based on underlying disease cohort. Results We identified 181 710 RA (mean age 55.3±13.1, 77% female), 45 834 SLE (47.1±13.1, 91% female), 30 307 PsA (49.7±11.5, 51% female), 7686 AS (44.6±12.0, 39% female) and parallel numbers of age-matched and sex-matched patients with HTN. The proportion of patients receiving long-term opioid prescriptions, and other measures of opioid prescriptions were higher among rheumatic disease cohorts and highest in patients with AS. AS was associated with the highest RR of receiving long-term opioid prescriptions (RR 2.73, 95% CI 2.60 to 2.87) versus HTN, while RRs were 2.21 (2.16 to 2.25) for RA, 1.94 (1.87 to 2.00) for PsA and 1.82 (1.77 to 1.88) for SLE. Conclusions Patients with rheumatic disease have higher rates of long-term opioid prescriptions, and patients with AS have the highest risk of receiving opioid prescriptions versus patients with HTN. Further studies investigating the effectiveness of disease-targeted treatments on decreasing opioid use in these four rheumatic diseases may provide strategies for reducing prescription opioids.
UNIX Systems Programming: Communication, Concurrency and Threads

This completely updated classic (originally titled Practical UNIX Programming) demonstrates how to design complex software to get the most from the UNIX operating system. UNIX Systems Programming provides a clear and easy-to-understand introduction tothe essentials of UNIX programming. Starting with short code snippetsthat illustrate how to use system calls, Robbins and Robbins movequickly to hands-on projects that help readers expand their skill levels.This practical guide thoroughly explores communication, concurrency,and multithreading. Known for its comprehensive and lucid explanations of complicated topics such as signals and concurrency, the book features practical examples, exercises, reusable code, and simplified libraries for use in network communication applications.A self-contained reference that relies on the latest UNIX standards,UNIX Systems Programming provides thorough coverage of files, signals,semaphores, POSIX threads, and client-server communication. Thisedition features all-new chapters on the Web, UDP, and server performance. The sample material has been tested extensively in theclassroom.
A comparison of parallel programming models for multiblock flow computations

Abstract A study is presented of the implementation of four different parallel programming models in a code that solves the fluid flow equations on block structured meshes. Performance results obtained on a number of distributed-memory parallel computer systems are given, in particular, for a 1024 processor Cray T3D system. Using the appropriate programming model, it is shown that excellent performance scaling can be obtained even for small problem sizes. The relative merits of each programming model in terms of ease of use, functionality, and performance are assessed.
Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels

Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas.
Activation of JAK/STAT Signaling in Megakaryocytes Sustains Myeloproliferation In Vivo

Purpose: The myeloproliferative neoplasms (MPN), including polycythemia vera, essential thrombocythemia, and primary myelofibrosis, are characterized by the expansion of the erythroid, megakaryocytic, and granulocytic lineages. A common feature of these disorders is the presence of abnormal megakaryocytes, which have been implicated as causative agents in the development of bone marrow fibrosis. However, the specific contributions of megakaryocytes to MPN pathogenesis remain unclear. Experimental Design: We used Pf4-Cre transgenic mice to drive expression of JAK2V617F in megakaryocyte lineage–committed hematopoietic cells. We also assessed the critical role of mutant megakaryocytes in MPN maintenance through cell ablation studies in JAK2V617F and MPLW515L BMT models of MPN. Results: JAK2V617F-mutant presence in megakaryocytes was sufficient to induce enhanced erythropoiesis and promote fibrosis, which leads to a myeloproliferative state with expansion of mutant and nonmutant hematopoietic cells. The increased erythropoiesis was associated with elevated IL6 level, which was also required for aberrant erythropoiesis in vivo. Furthermore, depletion of megakaryocytes in the JAK2V617F and MPLW515L BMT models ameliorated polycythemia and leukocytosis in addition to expected effects on megakaryopoiesis. Conclusions: Our observations reveal that JAK/STAT pathway activation in megakaryocytes induces myeloproliferation and is necessary for MPN maintenance in vivo. These observations indicate that MPN clone can influence the behavior of the wild-type hematopoietic milieu, at least, in part, via altered production of proinflammatory cytokines and chemokines. Our findings resonate with patients who present with a clinical MPN and a low JAK2V617F allele burden, and support the development of MPN therapies aimed at targeting megakaryocytes.
Motivations to Adopt Plant-Based Diets: Data from the Adhering to Dietary Approaches for Personal Taste (ADAPT) Study (P16-024-19).

Objectives To examine the differences in key motivations to adopt a dietary pattern (1) between self-reported plant-based diet followers and omnivores, and (2) among three types of plant-based diet followers: whole food, plant-based (WFPB), vegan, and vegetarian+pescatarian. Methods Adhering to Dietary Approaches for Personal Taste (ADAPT) is an online survey that recruits followers of popular diets. Of the 2010 enrolled participants, 1227 participants described their diet as plant-based, either WFPB (n = 705), vegan (n = 388), vegetarian (n = 103), or pescatarian (n = 31). The remaining 783 participants were categorized as omnivores. A multiple choice question with a free text option prompted participants to indicate their reasons for adhering to their self-identified dietary pattern, and a follow-up question asked them to rank their key motivations for adherence. The percentage of participants who chose each response as one of their top 2 key motivators was tabulated within each dietary pattern. Logistic regression, adjusted for age and gender, was used to compare the prevalence of top reasons among dietary patterns. The results were considered significant if <P = 0.05 after Bonferroni correction. Results The majority of both plant-based diet followers (79%) and of omnivores (83%) identified disease prevention and overall wellness as top motivations for following their dietary patterns. Significantly more plant-based diet followers, versus omnivores, chose helping the environment (17% vs. 4%) and supporting animal welfare (28% vs. 1%). Significantly more omnivores chose enjoyment (39% vs. 26%) and the need to address a specific health concern (44% vs. 29%). Significantly more WFPB followers (87%) chose disease prevention and overall wellness compared to vegans (71%) and vegetarians+pescatarians (66%). Significantly more vegans (47%) and vegetarians+pescatarians (33%) chose animal welfare than WFPB followers (15%). Conclusions The dietary motivations of plant-based diet followers are more diverse compared to those of omnivores. Among plant-based diet followers, WFPB followers often chose health motivations, and vegans, vegetarians, and pescatarians often chose ethical motivations. Funding Sources The Lisa Wendel Memorial Foundation, Tufts Collaborates Seed Grant, Tufts Summer Scholars Grant, and USDA ARS agreement No. 58-1950-4-003.