Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a modified prognostic index for patients with aggressive adult T-cell leukemia-lymphoma aged 70 years or younger: possible risk-adapted management strategies including allogeneic transplantation

Adult T-cell leukemia-lymphoma is a distinct type of peripheral T-cell lymphoma caused by human T-cell lymphotropic virus type I. Although allogeneic stem cell transplantation after chemotherapy is a recommended treatment option for patients with aggressive adult T-cell leukemia-lymphoma, there is no consensus about indications for allogeneic stem cell transplantation because there is no established risk stratification system for transplant eligible patients. We conducted a nationwide survey of patients with aggressive adult T-cell leukemia-lymphoma in order to construct a new, large database that includes 1,792 patients aged 70 years or younger with aggressive adult T-cell leukemia-lymphoma who were diagnosed between 2000 and 2013 and received intensive first-line chemotherapy. We randomly divided patients into two groups (training and validation sets). Acute type, poor performance status, high soluble interleukin-2 receptor levels (> 5,000 U/mL), high adjusted calcium levels (≥ 12 mg/dL), and high C-reactive protein levels (≥ 2.5 mg/dL) were independent adverse prognostic factors used in the training set. We used these five variables to divide patients into three risk groups. In the validation set, median overall survival for the low-, intermediate-, and high-risk groups was 626 days, 322 days, and 197 days, respectively. In the intermediate- and high-risk groups, transplanted recipients had significantly better overall survival than non-transplanted patients. We developed a promising new risk stratification system to identify patients aged 70 years or younger with aggressive adult T-cell leukemia-lymphoma who may benefit from upfront allogeneic stem cell transplantation. Prospective studies are warranted to confirm the benefit of this treatment strategy.
Country‐wide seroprevalence studies on Crimean‐Congo hemorrhagic fever and hantavirus infections in general population of Bulgaria

Crimean‐Congo hemorrhagic fever (CCHF) and hantavirus infections are the two viral hemorrhagic fevers spread in Europe. To test actual circulation of CCHF virus (CCHFV) and hantaviruses in Bulgaria, we conducted country‐wide seroepidemiological studies. Serum samples were collected prospectively from 1500 residents of all 28 districts in Bulgaria. CCHFV seroprevalence of 3.7% was revealed. Anamnesis for tick bites, contact with livestock, age over 40 years and residency in Haskovo district were found as risk factors. The highest CCHFV seroprevalence was observed in the known endemic districts in southeastern Bulgaria: Haskovo (28%) and Yambol (12%). Reactive samples were found in residents of 20 of the 28 districts in Bulgaria. In comparison with the previous studies, the data presented indicate that CCHFV increased substantially its circulation in the endemic regions and was introduced in many new areas. Hantavirus seroprevalence was based on results of the immunoblot and estimated as 3.1%. Surprisingly, contrary to all available data, Puumala virus seroprevalence rate was 2.3% versus 0.8% of Dobrava‐Belgrade virus. Evidence for hantavirus IgG seropositivity was found in residents of 23 of the 28 districts in the country. The first hantavirus seroprevalence study in Bulgaria showed that Puumala virus is probably more wide‐spread in the country than Dobrava‐Belgrade virus.
Accuracy of a New Swept-Source Optical Coherence Tomography Biometer for IOL Power Calculation and Comparison to IOLMaster.

PURPOSE To investigate the accuracy of the measurements provided by a new optical biometer (OA-2000, Tomey Corporation, Nagoya, Japan) for calculating the intraocular lens (IOL) power and to compare the refractive outcomes to those obtained with the IOLMaster 500 (Carl Zeiss Meditec, Jena, Germany). METHODS In this interventional multicenter study, consecutive patients having cataract surgery were enrolled. Only the IOL model used in the largest sample of patients was selected and the eyes implanted with that IOL were subsequently analyzed. The OA-2000, an optical biometer based on swept-source optical coherence tomography (SS-OCT), was used to measure axial length and corneal power in all eyes. IOL power was calculated with the Hoffer Q, Holladay 1, and SRK/T formulas. In a subsample of eyes, the IOL power was also calculated with measurements obtained by partial coherence interferometry (IOLMaster 500). The median absolute error and percentage of eyes with a prediction error of ±0.50 diopters (D) or less were calculated. RESULTS Two hundred forty-nine eyes were analyzed. Using SS-OCT, the median absolute error ranged between 0.33 (Holladay 1) and 0.35 (SRK/T) D. The rate of eyes with a prediction error of ±0.50 D or less ranged between 71.5% (Hoffer Q) and 67.1% (SRK/T). In the subsample of 87 eyes with measurements by both devices, the median absolute error was lower with the OA-2000 (Hoffer Q: P = .0377; Holladay 1: P = .0191; SRK/T: P = .0087). CONCLUSIONS The SS-OCT-based optical biometer investigated in the current study provides accurate measurements for IOL power calculation and seems to offer more predictable refractive results compared to the partial coherence interferometry IOLMaster. [J Refract Surg. 2017;33(10):690-695. ].
Habitat Use and Body Mass Regulation among Warblers in the Sahel Region during the Non-Breeding Season

Migratory birds face significant challenges across their annual cycle, including occupying an appropriate non-breeding home range with sufficient foraging resources. This can affect demographic processes such as over-winter survival, migration mortality and subsequent breeding success. In the Sahel region of Africa, where millions of migratory songbirds attempt to survive the winter, some species of insectivorous warblers occupy both wetland and dry-scrubland habitats, whereas other species are wetland or dry-scrubland specialists. In this study we examine evidence for strategic regulation of body reserves and competition-driven habitat selection, by comparing invertebrate prey activity-density, warbler body size and extent of fat and pectoral muscle deposits, in each habitat type during the non-breeding season. Invertebrate activity-density was substantially higher in wetland habitats than in dry-scrubland. Eurasian reed warblers Acrocephalus scirpaceus occupying wetland habitats maintained lower body reserves than conspecifics occupying dry-scrub habitats, consistent with buffering of reserves against starvation in food-poor habitat. A similar, but smaller, difference in body reserves between wet and dry habitat was found among subalpine warblers Sylvia cantillans but not in chiffchaffs Phylloscopus collybita inhabiting dry-scrub and scrub fringing wetlands. Body reserves were relatively low among habitat specialist species; resident African reed warbler A. baeticatus and migratory sedge warbler A. schoenobaenus exclusively occupying wetland habitats, and Western olivaceous warblers Iduna opaca exclusively occupying dry habitats. These results suggest that specialists in preferred habitats and generalists occupying prey-rich habitats can reduce body reserves, whereas generalists occupying prey-poor habitats carry an increased level of body reserves as a strategic buffer against starvation.
Does the Number of Pharmacies a Patient Frequents Affect Adherence to Statins?

BACKGROUND We hypothesized that medication adherence is affected by the number of pharmacies a patient frequents. OBJECTIVES The objective was to estimate the strength of association between the number of pharmacies a patient frequents and adherence to statins. METHODS Using administrative data from the Nova Scotia Seniors' Pharmacare program, a retrospective cohort study was conducted among subjects aged 65 years and older first dispensed statin between 1998 and 2008. The Usual Provider of Care (UPC), was defined as the number of dispensation days from the most frequented pharmacy divided by the total number of dispensation days. Estimated adherence of over 80% of the Medication Possession Ratio was defined as adherent. Data were analyzed using hierarchical linear regression. RESULTS The cohort of 25,641 subjects was 59% female with a mean age of 74 years. During follow-up, subjects filled prescriptions in a median of 2 (mean = 2; standard deviation = 0.88) pharmacies and visited pharmacies a median of 28 (mean = 30) times. During that time, 61% of patients used one pharmacy exclusively. Among subjects using 1 pharmacy, 59% were adherent while 58% using more than one pharmacy were adherent. However, upon adjustment for differences in distributions of age, sex, and other confounders, subjects who used more than one pharmacy had 10% decreased odds of statin adherence (odds ratio: 0.90, 95% confidence interval: 0.86-0.96). These results were robust in sensitivity analyses. CONCLUSIONS Among seniors newly starting statin therapy, using a single community pharmacy was modestly associated with adherence.
Ground Layer Plant Species Turnover and Beta Diversity in Southern-European Old-Growth Forests

Different assembly processes may simultaneously affect local-scale variation of species composition in temperate old-growth forests. Ground layer species diversity reflects chance colonization and persistence of low-dispersal species, as well as fine-scale environmental heterogeneity. The latter depends on both purely abiotic factors, such as soil properties and topography, and factors primarily determined by overstorey structure, such as light availability. Understanding the degree to which plant diversity in old-growth forests is associated with structural heterogeneity and/or to dispersal limitation will help assessing the effectiveness of silvicultural practices that recreate old-growth patterns and structures for the conservation or restoration of plant diversity. We used a nested sampling design to assess fine-scale species turnover, i.e. the proportion of species composition that changes among sampling units, across 11 beech-dominated old-growth forests in Southern Europe. For each stand, we also measured a wide range of environmental and structural variables that might explain ground layer species turnover. Our aim was to quantify the relative importance of dispersal limitation in comparison to that of stand structural heterogeneity while controlling for other sources of environmental heterogeneity. For this purpose, we used multiple regression on distance matrices at the within-stand extent, and mixed effect models at the extent of the whole dataset. Species turnover was best predicted by structural and environmental heterogeneity, especially by differences in light availability and in topsoil nutrient concentration and texture. Spatial distances were significant only in four out of eleven stands with a relatively low explanatory power. This suggests that structural heterogeneity is a more important driver of local-scale ground layer species turnover than dispersal limitation in southern European old-growth beech forests.
Changes in semantic fluency across childhood: Normative data from Australian-English speakers

Abstract Purpose: Verbal fluency tests are often used as part of an assessment battery to investigate children’s lexical knowledge as well as executive function skills. To date, however, issues surrounding consistency of measurement cloud comparisons across studies, with the developmental performance of Australian-English speaking children also currently lacking. This study tracked verbal fluency development as measured by two semantic fluency tasks that included coding of fluency, clustering and switching type responses. Method: Participants included 355 typically developing Australian-English speaking children (4–10 years) and 46 young adults. Total fluency was determined by the number of words produced for each category (Animals or Food), minus repetitions and rule violations. Semantic clusters (words generated within a subcategory) were coded while switches between single words or subcategories were differentiated and coded as either hard or cluster switches. Result: Fluency showed consistent improvement over age. Cluster Switches and Hard Switches showed some evidence of a plateau in performance relative to fluency, but in opposite direction. Other measures showed no strong trends over age. Results were similar for both semantic categories. Conclusion: Our results highlight the rich information available within a semantic fluency task and the importance of differentiating hard and cluster switches in paediatric samples.
The long non-coding RNA NEAT1 contributes to extracellular matrix degradation in degenerative human nucleus pulposus cells

Intervertebral disc degeneration is a complex disease involving genetic and environmental factors and multiple cellular processes. The role and expression of the lncRNA NEAT1 were assessed in intervertebral disc degeneration. NEAT1 expression was assessed in degenerative and control nucleus pulposus using RT-PCR. Western blotting and RT-PCR were also used to investigate p53 and p21 levels in nucleus pulposus tissues. NEAT1 function in degenerative nucleus pulposus cells was assessed with gain- and loss-of-function experiments. ERK/MAPK signaling was also examined. NEAT1, p53, and p21 were dramatically upregulated in intervertebral disc degeneration. Furthermore, catabolic MMP13 and ADAMTS5 were dysregulated and collagen II and aggrecan were downregulated after NEAT1 overexpression. This effect was reversed by transfection with si-NEAT1 in degenerative nucleus pulposus cells. In addition, NEAT1 was found to affect the activation of the ERK/MAPK pathway. The NEAT1-induced ECM degradation may involve ERK1/2/MAPK signaling. LncRNA NEAT1 may represent a novel molecular target for intervertebral disc degeneration treatment by preventing nucleus pulposus ECM degradation. Impact statement For the first time, our study demonstrates that lncRNA NEAT1 plays a role in the occurrence and development of IDD by participating in extracellular matrix remodeling. This lncRNA regulates catabolic MMP13 and ADAMTS5 and anabolic collagen II and aggrecan by affecting the ERK/MAPK signaling pathway in degenerative human nucleus pulposus (NP) cells. Our research provides a scientific basis for targeting of NEAT1 for the IDD.
Role of up-front autologous stem-cell transplantation in peripheral T-cell lymphoma for patients in response after induction: an analysis of patients from LYSA centers

Background Peripheral T-cell lymphoma (PTCL) remains a therapeutic challenge. Due to the rarity and the heterogeneity of PTCL, no consensus has been achieved regarding even the type of first-line treatment. The benefit of autologous stem-cell transplantation (ASCT) is, therefore, still intensely debated. Patients and methods In the absence of randomized trials addressing the role of ASCT, we performed a large multicentric retrospective study and used both a multivariate proportional hazard model and a propensity score matching approach to correct for sample selection bias between patients allocated or not to ASCT in intention-to-treat (ITT). Results Among 527 patients screened from 14 centers in France, Belgium and Portugal, a final cohort of 269 patients ≤65 years old with PTCL-not otherwise specified (NOS) (N = 78, 29%), angioimmunoblastic T-cell lymphoma (AITL) (N = 123, 46%) and anaplastic lymphoma kinase-positive anaplastic large cell lymphoma (ALK-ALCL) (N = 68, 25%) with partial (N = 52, 19%) or complete responses (N = 217, 81%) after induction was identified and information about treatment allocation was carefully collected before therapy initiation from medical records. One hundred and thirty-four patients were allocated to ASCT in ITT and 135 were not. Neither the Cox multivariate model (HR = 1.02; 95% CI: 0.69-1.50 for PFS and HR = 1.08; 95% CI: 0.68-1.69 for OS) nor the propensity score analysis after stringent matching for potential confounding factors (logrank P = 0.90 and 0.66 for PFS and OS, respectively) found a survival advantage in favor of ASCT as a consolidation procedure for patients in response after induction. Subgroup analyses did not reveal any further difference for patients according to response status, stage disease or risk category. Conclusions The present data do not support the use of ASCT for up-front consolidation for all patients with PTCL-NOS, AITL, or ALK-ALCL with partial or complete response after induction.
Preferential Occupancy of R2 Retroelements on the B Chromosomes of the Grasshopper Eyprepocnemis plorans

R2 non-LTR retrotransposons exclusively insert into the 28S rRNA genes of their host, and are expressed by co-transcription with the rDNA unit. The grasshopper Eyprepocnemis plorans contains transcribed rDNA clusters on most of its A chromosomes, as well as non-transcribed rDNA clusters on the parasitic B chromosomes found in many populations. Here the structure of the E. plorans R2 element, its abundance relative to the number of rDNA units and its retrotransposition activity were determined. Animals screened from five populations contained on average over 12,000 rDNA units on their A chromosomes, but surprisingly only about 100 R2 elements. Monitoring the patterns of R2 insertions in individuals from these populations revealed only low levels of retrotransposition. The low rates of R2 insertion observed in E. plorans differ from the high levels of R2 insertion previously observed in insect species that have many fewer rDNA units. It is proposed that high levels of R2 are strongly selected against in E. plorans, because the rDNA transcription machinery in this species is unable to differentiate between R2-inserted and uninserted units. The B chromosomes of E. plorans contain an additional 7,000 to 15,000 rDNA units, but in contrast to the A chromosomes, from 150 to over 1,500 R2 elements. The higher concentration of R2 in the inactive B chromosomes rDNA clusters suggests these chromosomes can act as a sink for R2 insertions thus further reducing the level of insertions on the A chromosomes. These studies suggest an interesting evolutionary relationship between the parasitic B chromosomes and R2 elements.
Perceived partner fertility desires and influence on contraceptive use*

Abstract Background: Perceived discordance of fertility desires may be more common among couples with certain sociodemographic characteristics and may lead to lower contraceptive use. Methods: Using nationally representative data from adults ages 15–49 in France in 2010, we analysed associations between sociodemographic characteristics, perceived discordance of fertility desires and contraceptive use with design-based logistic regression. Results: Only 8% of participants perceived discordant fertility desires while 92% perceived concordance with partner fertility desire. Discordance varied by age and relationship duration and by the presence of children from previous relationships. Perceived discordance was not associated with use of a hormonal or highly effective method. Beyond own intentions, perception of a partner’s fertility desires was associated with using a highly effective method among participants using any method. Conclusions: Engaging men and couples in family planning programmes may be important for achieving both partners’ desired fertility goals.
Association of Insurance Expansion With Surgical Management of Thyroid Cancer

Importance To our knowledge, thyroid cancer incidence is increasing faster than any other cancer type and is currently the fifth most common cancer among women. While this rise is likely multifactorial, there has been scarce consideration of the effect of insurance statuses on the treatment of thyroid cancer. Objective We evaluate the association of insurance expansion with thyroid cancer treatment using the 2006 Massachusetts health reform, which serves as a unique natural experiment. Design, Setting, and Participants We used the Agency for Healthcare Research and Quality State Inpatient Databases to identify patients with government-subsidized or self-pay insurance or private insurance who were admitted to a hospital with thyroid cancer and underwent a thyroidectomy between 2001 and 2011 in Massachusetts (n = 8534) and 3 control states (n = 48 047). Difference-in-differences models were used to evaluate an association between the 2006 Massachusetts health care reform and thyroid cancer treatment, and participants were controlled for age, sex, comorbidities, and secular trends. Main Outcomes and Measures Change in the thyroidectomy rate for thyroid cancer treatment was the primary outcome evaluated. Results The Massachusetts cohort consisted of 6443 women (75.5%) and 2091 men (24.5%), of whom 6388 (79.6%) were white, 391 (4.9%) were black, 527 (6.6%) were Hispanic, 424 (5.3%) were Asian/Pacific Islander, 63 (0.8%) were Native American, and 228 (2.8%) were other. The participants from control states included 36 818 women (76.6%) and 11 229 men (23.4%), of whom 30 432 (65.5%) were white, 3818 (8.2%) were black, 6462 (13.9%) were Hispanic, 2591 (5.6%) were Asian/Pacific Islander, 211 (0.5%) were Native American, and 2947 (6.3%) were other. Before the 2006 Massachusetts insurance expansion, patients with government-subsidized or self-pay insurance had lower thyroidectomy rates for thyroid cancer in Massachusetts and the control states compared with patients with private insurance. The Massachusetts insurance expansion was associated with a 26% increased rate of undergoing a thyroidectomy (incident rate ratio, 1.26; 95% CI, 1.04-1.52; P = .02) and a 22% increased rate of neck dissection (incident rate ratio, 1.22; 95% CI, 1.07-1.37; P = .002) for treating cancer compared with control states. Conclusions and Relevance The 2006 Massachusetts health reform, which is a model for the Affordable Care Act, was associated with a 26% increased rate of thyroidectomy for treating thyroid cancer. Our study suggests that insurance expansion may be associated with increased access to the surgical management of thyroid cancer. Further studies need to be conducted to evaluate the effect of healthcare expansion at a national level.
Proteomic investigation of the secretome of Cellvibrio japonicus during growth on chitin

Studies of the secretomes of microbes grown on insoluble substrates are important for the discovery of novel proteins involved in biomass conversion. However, data in literature and this study indicate that secretome samples tend to be contaminated with cytoplasmic proteins. We have examined the secretome of the Gram‐negative soil bacterium Cellvibrio japonicus using a simple plate‐based culturing technique that yields samples with high fractions (60–75%) of proteins that are predicted to be secreted. By combining this approach with label‐free quantification using the MaxLFQ algorithm, we have mapped and quantified proteins secreted by C. japonicus during growth on α‐ and β‐chitin. Hierarchical clustering of the detected protein quantities revealed groups of up‐regulated proteins that include all five putative C. japonicus chitinases as well as a chitin‐specific lytic polysaccharide monooxygenase (CjLPMO10A). A small set of secreted proteins were co‐regulated with known chitin‐specific enzymes, including several with unknown catalytic functions. These proteins provide interesting targets for further studies aimed at unraveling the enzymatic machineries used by C. japonicus for recalcitrant polysaccharide degradation. Studies of chitin degradation indicated that C. japonicus indeed produces an efficient chitinolytic enzyme cocktail. All MS data have been deposited in the ProteomeXchange with the dataset identifier PXD002843 (http://proteomecentral.proteomexchange.org/dataset/PXD002843).