Miracle-dz/UniFAR-FTUs huggingface dataset:
Seminal bacterial composition in patients with obstructive and non-obstructive azoospermia

A number of culture-dependent and -independent studies have reported that the number and significance of bacterial species in semen may have been underestimated. The aim of the present study was to profile the seminal microbiome in patients with obstructive or non-obstructive azoospermia. A high-throughput sequencing method was adopted to sequence genomic DNA extracted from the semen of healthy people (C group), patients with obstructive azoospermia (OA group) and patients with non-obstructive azoospermia (NOA group). The results revealed that Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria species comprised the majority of bacteria in the C (98.14%), OA (98.26%) and NOA (90.96%) groups. Patients in the OA and NOA groups exhibited an increase in Bacteroidetes and Firmicutes, whereas the number of Proteobacteria and Actinobacteria were decreased compared with the C group. A total of 398 common operational taxonomic units were identified, of which 27 belonged to the genus Lactobacillus. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis indicated that the pathogenic species and reduced biodiversity in the semen of patients with azoospermia may result in an increased risk of metabolic, infectious and immune diseases. In the present study, the seminal microbiome of patients with obstructive or non-obstructive azoospermia was explored, which may be useful for developing novel treatments against azoospermia as well as for its diagnosis.
An interobserver reliability comparison between the Orthopaedic Trauma Association's open fracture classification and the Gustilo and Anderson classification

Aims To evaluate interobserver reliability of the Orthopaedic Trauma Association's open fracture classification system (OTA‐OFC). Patients and Methods Patients of any age with a first presentation of an open long bone fracture were included. Standard radiographs, wound photographs, and a short clinical description were given to eight orthopaedic surgeons, who independently evaluated the injury using both the Gustilo and Anderson (GA) and OTA‐OFC classifications. The responses were compared for variability using Cohen's kappa. Results The overall interobserver agreement was &kgr; = 0.44 for the GA classification and &kgr; = 0.49 for OTA‐OFC, which reflects moderate agreement (0.41 to 0.60) for both classifications. The agreement in the five categories of OTA‐OFC was: for skin, &kgr; = 0.55 (moderate); for muscle, &kgr; = 0.44 (moderate); for arterial injury, &kgr; = 0.74 (substantial); for contamination, &kgr; = 0.35 (fair); and for bone loss, &kgr; = 0.41 (moderate). Conclusion Although the OTA‐OFC, with similar interobserver agreement to GA, offers a more detailed description of open fractures, further development may be needed to make it a reliable and robust tool.
Tea Polyphenols and Prevention of Epigenetic Aberrations in Cancer

Tea polyphenols are secondary metabolites of tea plants and are well known for beneficial health effects. They can protect from a variety of illnesses including cancers. Tea polyphenols can prevent cancer by modulating epigenetic aberrations taking place in DNA methylation, histone modifications, and micro-RNAs. By altering these epimutations, they regulate chromatin dynamics and expression of genes those induce or suppress cancer formation. However, majority of the studies in existing literature are carried out for green tea polyphenols rather than black tea polyphenols despite the fact that black tea is the most commonly consumed form of tea (78%) followed by green tea (20%) and other forms of tea. Research findings indicate that tea polyphenols may be potential source from which drugs with less side effects and affordable price can be developed.
Mesoscopic Modeling of Stochastic Reaction-Diffusion Kinetics in the Subdiffusive Regime

Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model of subdiffusion into an accurate and consistent reaction-subdiffusion computational framework. Two different possible models of chemical reaction are revealed and some basic dynamic properties are derived. In certain cases those mesoscopic models have a direct interpretation at the macroscopic level as fractional partial differential equations in a bounded time interval. Through analysis and numerical experiments we estimate the macroscopic effects of reactions under subdiffusive mixing. The models display properties observed also in experiments: for a short time interval the behavior of the diffusion and the reaction is ordinary, in an intermediate interval the behavior is anomalous, and at long times the behavior is ordinary again.
Mechanical characterization of unidirectional CFRP thin strip and CFRP cables under quasi-static and dynamic tension

Under uniaxial tension, full stress-strain curves up to fracture and mechanical properties of a variety of CFRP cables having different structures are evaluated experimentally at three strain rates ranging from quasi-static (10-5 s-1) to dynamic (102 s-1). Such properties as tensile strength, chord or tangent modulus, strain at tensile strength and absorbed energy per unit volume are obtained. Experimental difficulties on stress and strain measurements and specimen fastening are overcome by introducing special instrumental arrangements and an expansive-cement fastening technique. For all cables, at quasi-static (10-5 s-1) and intermediate (10-2 s-1) strain rates, the stress-strain relation is linear. On the other hand, at a dynamic (102 s-1) strain rate, the stress-strain relation is non-linear and all cables tend to increase their elastic modulus and tensile strength. This obviously leads to increase of the absorbed energy per unit volume under dynamic tension. However, the strain at tensile strength remains almost the same at all strain rates. Thus, from a consideration based on the fracture strain criterion, it is concluded that strain rate insensitivity is assured for all cables.
In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality

Diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (OMP) family in Gram-negative bacteria. Differences in pore size and amino acid composition contribute to the specificity. Structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. Entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, specificity and biological niche adaptation. The high mutation rate in their surface-exposed loops is likely an important mechanism for host immune system evasion. Multiple sequence alignments for each subclass revealed conserved residue positions that are involved in substrate recognition and specificity. An analysis of monomeric protein channels revealed particular sequence patterns of amino acids that were observed in other classes at multimeric interfaces. This adds to the emerging evidence that all members of the family exist in a multimeric state. Our findings are important for understanding the role of members of this family in a wide range of bacterial processes, including bacterial food uptake, survival and adaptation mechanisms.
Establishing sickle cell diagnostics and characterizing a paediatric sickle cell disease cohort in Malawi

poor accrual. In summary, this study provides preliminary data on the efficacy of the combination of alisertib and bortezomib for relapsed MM. The duration of response varied widely with one patient staying on therapy for more than 3 years. Nevertheless, the contribution of alisertib to bortezomib activity cannot be determined without additional Phase II testing. Further studies looking at inhibition of Aurora kinase A alone or in combination with established or novel anti-MM therapies will be necessary.
Rab27a Is Required for Regulated Secretion in Cytotoxic T Lymphocytes

Rab27a activity is affected in several mouse models of human disease including Griscelli (ashen mice) and Hermansky-Pudlak (gunmetal mice) syndromes. A loss of function mutation occurs in the Rab27a gene in ashen (ash), whereas in gunmetal (gm) Rab27a dysfunction is secondary to a mutation in the α subunit of Rab geranylgeranyl transferase, an enzyme required for prenylation and activation of Rabs. We show here that Rab27a is normally expressed in cytotoxic T lymphocytes (CTLs), but absent in ashen homozygotes (ash/ash). Cytotoxicity and secretion assays show that ash/ash CTLs are unable to kill target cells or to secrete granzyme A and hexosaminidase. By immunofluorescence and electron microscopy, we show polarization but no membrane docking of ash/ash lytic granules at the immunological synapse. In gunmetal CTLs, we show underprenylation and redistribution of Rab27a to the cytosol, implying reduced activity. Gunmetal CTLs show a reduced ability to kill target cells but retain the ability to secrete hexosaminidase and granzyme A. However, only some of the granules polarize to the immunological synapse, and many remain dispersed around the periphery of the CTLs. These results demonstrate that Rab27a is required in a final secretory step and that other Rab proteins also affected in gunmetal are likely to be involved in polarization of the granules to the immunological synapse.
No-Show for Treatment in Substance Abuse Patients with Comorbid Symptomatology: Validity Results from a Controlled Trial of the ASAM Patient Placement Criteria

Purpose:Mismatched placement, according to the American Society of Addiction Medicine's (ASAM) Patient Placement Criteria (PPC), promotes no-shows to treatment; however, little is known about the impact on patients with psychiatrically comorbid substance use disorder. Methods:In a multisite trial, public-sector treatment-seeking adults (N = 700), following a computer-assisted ASAM PPC-1 structured interview, were blindly scored and randomly assigned to Level-of-Care (LOC)-II (intensive outpatient) or LOC-III (residential) settings. Patients scored as needing LOC-II but assigned to LOC-III were, by definition, “overmatched. ” Results:Among 143 overmatched patients, no-shows were significantly higher in comorbids versus noncomorbids (54% versus 28%; P < 0.01). Among overmatched comorbids, patients who no-showed compared with patients who showed were more likely to be females (70.4% versus 34.8%; P < 0.05), to have anxiety (63% versus 17.4%; P < 0.01), or have supportive family/social environments (81.5% versus 34.8%; P < 0.01). Conclusions:The data support the validity of the PPC for matching comorbid patients. Mismatching increases no-show rates in general with undermatching, but it does so in particular with overmatching in patients with comorbid psychiatric symptomatology. Comorbidity interacts with gender, overmatched status, presence of anxiety, and supportive environment as predictors of treatment no-shows (odds ratios = 2.69, P < 0.05; 3.27, P < 0.05; 5.32, P < 0.001; and 3.12, P < 0.05, respectively).
Rosmarinic Acid Activates AMPK to Inhibit Metastasis of Colorectal Cancer

Rosmarinic acid (RA) has been used as an anti-inflammatory, anti-diabetic, and anti-cancer agent. Although RA has also been shown to exert an anti-metastatic effect, the mechanism of this effect has not been reported to be associated with AMP-activated protein kinase (AMPK). The aim of this study was to elucidate whether RA could inhibit the metastatic properties of colorectal cancer (CRC) cells via the phosphorylation of AMPK. RA inhibited the proliferation of CRC cells through the induction of cell cycle arrest and apoptosis. In several metastatic phenotypes of CRC cells, RA regulated epithelial–mesenchymal transition (EMT) through the upregulation of an epithelial marker, E-cadherin, and the downregulation of the mesenchymal markers, N-cadherin, snail, twist, vimentin, and slug. Invasion and migration of CRC cells were inhibited and expressions of matrix metalloproteinase (MMP)-2 and MMP-9 were decreased by RA treatment. Adhesion and adhesion molecules such as ICAM-1 and integrin β1 expressions were also reduced by RA treatment. In particular, the effects of RA on EMT and MMPs expressions were due to the activation of AMPK. Moreover, RA inhibited lung metastasis of CRC cells by activating AMPK in mouse model. Collectively, these results proved that RA could be potential therapeutic agent against metastasis of CRC.
Thiazide diuretics and the risk of osteoporotic fractures in hypertensive patients. Results from the Swedish Primary Care Cardiovascular Database

Objective: The objective is to investigate if treatment with thiazides reduces the risk of osteoporotic fractures in hypertensive patients in primary healthcare. Further we aimed to examine the impact of duration of thiazide use, the consequences of discontinuation of treatment, and the possible difference in effect between men and women. Method: This retrospective cohort study includes 57 822 individuals, 45 years and older, diagnosed with hypertension during 2001–2008 in the Swedish Primary Care Cardiovascular Database. Patients were followed from 1 January 2006 (or the date of their first diagnosis of hypertension if that date came later), until they had an incident osteoporotic fracture, died, or reached the end of the study at 31 December 2012. Patients exposed to thiazides were compared with patients never exposed to thiazides. Results: Current use of thiazides was associated with significantly reduced risk of osteoporotic fractures [hazards ratio 0.89; 95% confidence interval (CI) 0.81–0.98], and increased with longer treatment periods (hazards ratio 0.87; 95% CI 0.78–0.97 after 2 years). However, discontinuation of thiazides increased the risk of osteoporotic fractures (hazards ratio 1.18; 95% CI 1.04–1.33), but attenuated with longer duration past treatment period. When analyzing men and women separately, similar results were seen, although only significant in men. Conclusion: This large observational study confirms that thiazide therapy in hypertensive patients is associated with a reduced risk of osteoporotic fractures. The protective effect increased with longer treatment periods. However, discontinuation of treatment increased the risk of fractures, which emphasizes the importance of continuous treatment.
DNA methylation immediately adjacent to active histone marking does not silence transcription

Active promoters generally contain histone H3/H4 hyperacetylation and tri-methylation at H3 lysine 4, whereas repressed promoters are associated with DNA methylation. Here we show that the repressed erythroid-specific carbonic anhydrase II (CAII) promoter has active histone modifications localized around the transcription start, while high levels of CpG methylation are present directly upstream from these active marks. Despite the presence of active histone modifications, the repressed promoter requires hormone-induced activation for efficient preinitiation complex assembly. Transient and positional changes in histone H3/H4 acetylation and local changes in nucleosome density are evident during activation, but the bipartite epigenetic code is stably maintained. Our results suggest that active histone modifications may prevent spreading of CpG methylation towards the promoter and show that repressive DNA methylation immediately adjacent to a promoter does not necessarily repress transcription.
Charring of protected wood studs

The charring of wood studs has been studied in the cone calorimeter at constant heat flax 50 kW/m(2) and compared to data from full-scale furnace wall tests. The wood studs were unprotected or protected by gypsum plasterboards on the exposed side. Similar charring depths were found and the data analysed mainly in terms of fire exposure. A simple small-scale technique was developed to measure the heat transfer through protective boards and tbe charring depth of wood studs. These properties are essential for the load bearing capacity of wood frame structures.
Actin cytoskeleton remodeling during early Drosophila furrow formation requires recycling endosomal components Nuclear-fallout and Rab11

Cytokinesis requires a dramatic remodeling of the cortical cytoskeleton as well as membrane addition. The Drosophila pericentrosomal protein, Nuclear-fallout (Nuf), provides a link between these two processes. In nuf-derived embryos, actin remodeling and membrane recruitment during the initial stages of metaphase and cellular furrow formation are disrupted. Nuf is a homologue of arfophilin-2, an ADP ribosylation factor effector that binds Rab11 and influences recycling endosome (RE) organization. Here, we show that Nuf is an important component of the RE, and that these phenotypes are a consequence of Nuf activities at the RE. Nuf exhibits extensive colocalization with Rab11, a key RE component. GST pull-downs and the presence of a conserved Rab11-binding domain in Nuf demonstrate that Nuf and Rab11 physically associate. In addition, Nuf and Rab11 are mutually required for their localization to the RE. Embryos with reduced levels of Rab11 produce membrane recruitment and actin remodeling defects strikingly similar to nuf-derived embryos. These analyses support a common role for Nuf and Rab11 at the RE in membrane trafficking and actin remodeling during the initial stages of furrow formation.
Time interval effect on repeat cervical smear results.

OBJECTIVE Second cervical smears obtained at short time intervals often exhibit a lesser degree of abnormality than the first smear. We studied the effect of time interval between smears on diagnoses in two large, distinctive cohorts. STUDY DESIGN Patients with two or more satisfactory smears with at least one smear or a cervical biopsy showing atypical squamous cells of undetermined significance or greater were selected. Patients were divided into four subsets by test intervals (days) (< or = 45, 46-90, 91-120, > 120) and compared statistically. RESULTS The distribution of differences between results for the short-interval subsets (< 120) was significantly different (P < .01) from the interval subset > 120 days. At short intervals the results revealed loss of sensitivity in the second smear as compared to the initial smear and concurrent biopsies. CONCLUSION Rapidly repeated cervical smears show poor agreement with the biopsy and may be misleading. This effect is most pronounced when the interval is < 45 days. Colposcopists should consider whether concurrent smears shortly after an abnormal smear are worth performing, given the loss of sensitivity.
Effects of core needle biopsy and subsequent neoadjuvant chemotherapy on molecular alterations and outcome in breast cancer

Objectives The aim of our study is to evaluate the effect of core needle biopsy (CNB) and subsequent neoadjuvant chemotherapy (NAC) on the expression of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth hormone receptor 2 (HER2) and Ki67 in breast cancer, and the associated influencing factors. Materials and methods In this retrospective cohort study, 143 patients with primary operable breast cancer who received NAC were included. ER, PR, HER2 and Ki67 statuses were compared between pretreatment and posttreatment residual samples. A control group of paired core and excision tumors from 123 patients who did not receive NAC within the same study period was also assessed. Data on patients’ clinicopathologic features were collected to identify associated influencing factors. Results Ki67 value significantly increased in excision tumors compared with paired core samples in controls without presurgery treatment (P<0.01), which was associated with the pathologic lymph node status and the interaction of PR and HER2 status (P=0.008 and 0.028, respectively). In 143 patients who underwent NAC, a significant decrease was observed in the expression of PR and Ki67 after NAC (P=0.003 and P<0.01, respectively). Further subgroup analysis showed that PR decrease was more obvious in premenopausal patients and Luminal A patients (P=0.006 and 0.002, respectively). Conclusion Core samples could provide more reliable information on determination of molecular subtype than surgical excisions. Decreases in PR and Ki67 expression following NAC could be used as positive prognostic factors. We recommend repeat testing of these biologic markers following NAC for the sake of better disease management. To the best of our knowledge, this is the most comprehensive study to analyze the effect of neoadjuvant chemotherapy on molecular alteration and its associated influencing factors after reporting a CNB-associated Ki67 increase in the same study.
Musculoskeletal complaints in individuals with finger or partial hand amputations in the Netherlands: a cross-sectional study

Abstract Purpose: To compare the prevalence of musculoskeletal complaints (MSCs) in individuals with finger or partial hand amputations (FPHAs) with a control group and to explore the effect and predictors of MSCs in individuals with FPHAs. Method: A questionnaire-based cross-sectional study was conducted. The primary outcome measures were: prevalence of MSCs, health status, pain-related disability, physical work demands, work productivity, and hand function. Results: The response rate was 61%. A comparable proportion of individuals with FPHAs (n = 99) and controls (n = 102) reported MSCs in the preceding 4 weeks (33% vs. 28%, respectively) or in the preceding year (37% vs. 33%, respectively). Individuals with FPHAs with MSCs experienced more pain than controls with MSCs. Regular occurrence of stump sensations and self-reported limited range of motion (ROM) of the wrist of the affected limb were predictors for MSCs in individuals with FPHAs. Conclusions: The prevalence of MSCs was comparable in individuals with FPHAs and controls. However, clinicians should pay special attention to the risk of developing MSCs in patients with stump sensations and limited ROM of the wrist of the affected limb. Future research should focus on the role of wrist movements and compensatory movements in the development of MSCs in individuals with FPHAs. Implications for Rehabilitation The prevalence of musculoskeletal complaints (MSCs) in individuals with finger or partial hand amputations (FPHAs) and control subjects was similar. Regular occurrence of stump sensations and limited range of motion of the wrist of the affected limb were predictors of developing MSCs in individuals with FPHAs. Clinicians should pay special attention to individuals with FPHAs with the presence of these predictors of developing MSCs. For a better understanding of the development of and treatment options for MSCs, future research focusing on the role of wrist function in the development of MSCs in individuals with FPHAs is necessary.
Groups, measures, and the NIP

We discuss measures, invariant measures on definable groups, and genericity, often in an NIP (failure of the independence property) environment. We complete the proof of the third author’s conjectures relating definably compact groups G in saturated o-minimal structures to compact Lie groups. We also prove some other structural results about such G, for example the existence of a left invariant finitely additive probability measure on definable subsets of G. We finally introduce a new notion “compact domination” (domination of a definable set by a compact space) and raise some new conjectures in the o-minimal case.