Miracle-dz/UniFAR-FTUs huggingface dataset:
What Does a Single Semen Sample Tell You? Implications for Male Factor Infertility Research

Semen parameters are variable within individuals, but it is unclear whether 1 semen sample could represent a man's long-term average values in epidemiologic studies. Between 2005 and 2014, a total of 329 men from a fertility clinic in Boston, Massachusetts, provided 768 semen samples as part of the Environment and Reproductive Health (EARTH) Study. Total sperm count, sperm concentration, morphology, motility, and ejaculate volume were assessed. We used linear mixed models to compare values from men's first semen samples with their long-term averages and to calculate intraclass correlation coefficients for each parameter. We calculated positive predictive values (PPVs) and negative predictive values (NPVs) by comparing agreement in classification according to World Health Organization reference limits. There were no differences in mean semen parameters between men's first samples and the remaining replicates. Intraclass correlation coefficients ranged from 0.61 for morphology to 0.75 for concentration, indicating consistently greater between-man variability than within-man variability. Nevertheless, using 1 sample alone resulted in high NPVs but low PPVs (range, 43%-91%). The average of 2 samples was needed to achieve high PPVs (range, 86%-100%) and NPVs (range, 91%-100%). We conclude that 1 semen sample may suffice for studies aimed at identifying average differences in semen quality between individuals. Studies aimed at classifying men based on World Health Organization reference limits may benefit from collection of 2 or more samples.
Effect of positive heel inclination on posture.

Millions of women wear high heels on a daily basis; however, few studies have analyzed the changes high heels (positive heel inclination) have on posture. The purpose of this study was to determine whether positive heel inclination changed the postural alignment of the head, spine, pelvis, and knees. Fifteen female college students ((mean age = 22.7, SD = 3.7 years) had sagittal plane angles measured for the cervical spine, thoracic spine, lumbar spine, sacral spine, and knee joints in addition to anterior/posterior displacements of the head and pelvis. All variables were assessed by a Metrecom Skeletal Analysis System, a three-dimensional electrogoniometer. Six randomized trials, three at zero heel inclination and three at 5 cm positive heel inclination, were measured. Analysis of variance results indicated positive heel inclination of subjects brought about significantly lower anterior pelvic tilt, lumbar lordosis, and sacral base angles when compared with zero heel inclination (p < .01). Clinically, patients with low back pain may be affected by high heel usage because of the reduction of the normal lumbar lordosis.
Pre-steady-state Kinetics for Hydrolysis of Insoluble Cellulose by Cellobiohydrolase Cel 7 A *

Nicolaj Cruys-Bagger, Jens Elmerdahl, Eigil Praestgaard, Hirosuke Tatsumi, Nikolaj Spodsberg, Kim Borch, and Peter Westh From the Research Unit for Functional Biomaterials, Department of Science, Systems, and Models, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark, the International Young Researchers Empowerment Center, Shinshu University, Matsumoto, Nagano 390-8621, Japan, and Novozymes A/S, Krogshøjvej 36, 2880 Bagsvaerd, Denmark
XMM-Newton Observations of Red AGNs

XMM-Newton spectra of five red 2MASS active galactic nuclei (AGNs), selected from a sample observed by Chandra to be relatively X-ray bright and to cover a range of hardness ratios, confirm the presence of substantial absorbing material in three sources with optical classifications ranging from type 1 to type 2. A flat (hard) power-law continuum is observed in the other two. The combination of X-ray absorption and broad optical emission lines suggests either a small (nuclear) absorber or a favored viewing angle so as to cover the X-ray source but not the broad emission-line region (BELR). A soft excess is detected in all three type 1 sources. We speculate that this may arise in an extended region of ionized gas, perhaps linked to the polarized (scattered) optical light present in these sources. The spectral complexity revealed by XMM-Newton emphasizes the limitations of the low-S/N Chandra data. The new results strengthen our earlier conclusions that the observed X-ray continua of red AGNs are unusually hard at energies ≳2 keV. Their observed spectra are consistent with contributing significantly to the missing hard or absorbed population of the cosmic X-ray background (CXRB), although their intrinsic power-law slopes are typical of broad-line (type 1) AGNs (Γ ~ 1.7-1.9). This suggests that the missing X-ray-absorbed CXRB population may include type 1 AGNs or QSOs in addition to the type 2 AGNs generally assumed.
Functional Differences between Subpopulations of Mobilized Peripheral Blood‐Derived CD34+ Cells Expressing Different Levels of HLA‐DR, CD33, CD38 and c‐kit Antigens

We have investigated the functional characteristics of peripheral blood‐derived CD34+ cells mobilized by a combination of chemotherapy and G‐CSF (mobilized peripheral blood‐derived [MPB] CD34+ cells). In this study, subpopulations of MPB CD34+ cells have been directly compared in clonal cultures, long‐term cultures with bone marrow (BM) stromal cells, and single‐cell cultures. MPB CD34+ cells could be subdivided by expression levels of HLA‐DR (DR), CD38, CD33 and c‐kit antigens. The majority of MPB CD34+ cells expressed DR and CD38 antigens. In contrast, approximately 60% and 20% of the MPB CD34+ cells expressed CD33 and c‐kit antigens, respectively. Interestingly, MPB CD34+ cells can be subdivided into three fractions which express high, low or negative levels of c‐kit receptor. All types of committed progenitors were observed in populations of CD34+DR+, CD34+DR−, CD34+CD33−, CD34+CD38+ and CD34+ c‐kitlow cells. Colony forming unit‐granulocyte/macrophage was highly enriched in the population of CD34+CD33+ cells, whereas BFU‐E was highly enriched in the population of CD34+ c‐kithigh cells. In the population of CD34+CD38− cells, however, a few myeloid progenitors were detected. In addition, limiting dilution analyses clearly showed that the long‐term culture‐initiating cell (LTC‐IC) is enriched in the populations of CD34+DR−, CD34+CD33− and CD34+c‐kit− or low cells, but very few in CD34+ c‐kithigh cells, and that CD38 antigen is not a useful marker for the enrichment of LTC‐IC derived from MPB CD34+ cells. Moreover, single cell clone sorting experiments clearly demonstrated the functional differences between CD34+CD38+ and CD34+CD38− cells as well as CD34+ cells expressing different levels of c‐kit receptor. Our results suggest that an immunophenotype of LTC‐IC is different between BM‐, cord blood‐ and MPB‐derived CD34+ cells and that primitive and committed progenitors existing in these sources may be functionally different.
Progressive supranuclear palsy

Twelve patients with progressive supranuclear palsy were treated with methysergide; the response was monitored with videotaped examination, electrooculography, and psychometric assessment. Used alone and with antiparkinsonian agents, methysergide improved the quality of life in eight patients for 6 months to 2 years. Benefits were especially dramatic in four patients with severe dysphagia. The disorder of visually guided behavior included abnormal orienting responses, visuosocial expression and regard, and visual search. Mesencephalic visuomotor centers appear to be important not only in control of ocular motility but also in the elaboration of visually guided behavior and the orienting of spatial attention.
Clostridial VirR/VirS regulon involves a regulatory RNA molecule for expression of toxins

We analysed the region encoding VR‐RNA (VirR‐regulated RNA), which has been reported to be positively regulated by the two‐component VirR/VirS system in Clostridium perfringens. The VR‐RNA promoter identified by primer extension analysis was preceded by a probable VirR‐binding site (CCAGTTNNNCAC), which resembled a repeated sequence motif present in the promoter region of the theta‐toxin (pfoA) gene. A VR‐RNA‐null mutant, constructed by a homologous recombination, exhibited a reduced amount of transcription of the alpha‐ (plc) and kappa‐toxin (colA) genes, which was restored by the complementation of intact VR‐RNA, indicating that the VR‐RNA region plays an important role in the regulation of the plc and colA genes in C. perfringens. It was found that the regulatory effect was observed even when the hyp7 gene encoded on VR‐RNA was deleted or a nonsense mutation was introduced in the hyp7‐coding region. We found that the small 3′‐portion of VR‐RNA was sufficient for the activation of toxin genes, which suggested that VR‐RNA itself could act as an RNA regulatory molecule for the plc and colA genes mediating the regulatory information from the VirR/VirS system in C. perfringens.
Interference Between Units in Randomized Experiments

In a randomized experiment comparing two treatments, there is interference between units if applying the treatment to one unit may affect other units. Interference implies that treatment effects are not comparisons of two potential responses that a unit may exhibit, one under treatment and the other under control, but instead are inherently more complex. Interference is common in social settings where people communicate, compete, or spread disease; in studies that treat one part of an organism using a symmetrical part as control; in studies that apply different treatments to the same organism at different times; and in many other situations. Available statistical tools are limited. For instance, Fisher's sharp null hypothesis of no treatment effect implicitly entails no interference, and so his randomization test may be used to test no effect, but conventional ways of inverting the test to obtain confidence intervals, say for an additive effect, are not applicable with interference. Another commonly used approach assumes that interference is of a simple parametric form confined to units that are near one another in time or space; this is useful when applicable but is of little use when interference may be widespread and of uncertain form. Exact, nonparametric methods are developed for inverting randomization tests to obtain confidence intervals for magnitudes of effect assuming nothing at all about the structure of the interference between units. The limitations of these methods are discussed. To illustrate the general approach, two simple methods and two simple empirical examples are discussed. Extension to randomization based covariance adjustment is briefly described.
Interference of IgA Protease with the Effect of Secretory IgA on Adherence of Oral Streptococci to Saliva-coated Hydroxyapatite

It has previously been shown that secretory immunoglobulin A (S-IgA) influences the sorption of oral streptococci to hydroxyapatite as well as to cell surfaces. The present experiments demonstrate that bacterial IgA proteases, which cleave S-IgA in the hinge region, are capable of interfering with this mechanism. This result was obtained with an IgAI specific protease from Hæmophilus influenzae and with a protease from Clostridium ramosum that cleaves IgAI as well as IgA2 of A2m(I) allotype. The modulation of S-IgA-mediated effects by IgA proteases were studied by means of an in vitro method which permits quantitative determination of the sorption of radiolabeled oral bacteria to hydroxyapatite beads. Other authors have suggested that IgA protease-mediated effects may be explained by a strongly reduced antigen-binding capacity of released Fabα fragments. Here we present evidence that streptococci, after exposure to specific S-IgA and IgA protease, are coated with Fab α fragments.
Infectious mononucleosis patients temporarily recognize a unique, cross‐reactive epitope of Epstein‐Barr virus nuclear antigen‐1

The spectrum of antibodies against Epstein‐Barr virus nuclear antigen‐1 (EBNA‐1) in patients with a recent history of infectious mononucleosis and nonaffected EBV‐positive individuals has been characterized by epitope mapping. Sera were evaluated for antibodies to all unique maximally overlapping octapeptides of EBNA‐1. Both normal controls and patients with infectious mononucleosis produce IgG antibodies that recognize the glycine‐alanine‐rich portion of EBNA‐1, as previously described. All EBNA‐1 IgG‐positive infectious mononucleosis patients tested, however, consistently produce IgG specific for an additional epitope (aa 398–412 PPPGRRPFFHPVGEA) near the middle of the EBNA‐1 protein. This region was not found to be antigenic in healthy EBV‐seropositive individuals. This region does, however, cross‐react with the sequence PPPGMRPP from the common lupus spliceosomal autoantigen Sm B′ in several infectious mononucleosis patient sera. Patients with recent clinical infectious mononucleosis temporarily recognize a unique cross‐reactive epitope of EBNA‐1 not bound by antibodies from non‐infectious mononucleosis EBV‐positive sera or those with a distant history of IM. J. Med. Virol. 70: 253–257, 2003. © 2003 Wiley‐Liss, Inc.
Highlights of Latest American College of Cardiology and American Heart Association Guidelines for Management of Patients with Acute Myocardial Infarction

The recently published American College of Cardiology/American Heart Association Guidelines for the Management of Patients with Acute Myocardial Infarction stress 3 major points: (1) the prehospital phase from the onset of symptoms to definitive therapy in the emergency department must be shortened by 50% in order to reduce further the estimated 30% mortality rate for all patients in the community who suffer an acute myocardial infarction; (2) a more widespread use of thrombolytic agents is warranted because of the demonstrated, extremely time-dependent benefit to survivorship: the sooner it is given, the better the outcome; and (3) the administration of aspirin (160–325 mg) daily for an indefinite period is perhaps the most important therapy for a patient with acute myocardial infarction. Long-term therapy with lipid-lowering Statin drugs and angiotensin-converting enzyme inhibitor agents are gaining increasing evidence-based data to support their perpetual use as well.
A Multidimensional Physical Self-concept and Its Relations to Multiple Components of Physical Fitness

This study examines relations between six components of physical self-concept (Endurance, Balance, Flexibility, Strength, Appearance, and general Physical Ability) and five components of physical fitness (Endurance, Balance, Flexibility, Static Strength, Explosive Strength/Power) for a sample (N = 105) of young adolescent girls aged 13 and 14. Hierarchical confirmatory factor analyses identified the six physical self-concept scales and provided support for a multidimensional, hierarchical model of physical self-concept. The pattern of correlations between specific components of physical self-concept and physical fitness generally supported the construct validity of the self-concept responses, and the correlation between second-order factors representing general physical self-concept and general physical fitness (r = .76) was substantial.
NLM at ImageCLEF 2017 Caption Task

This paper describes the participation of the U.S. National Library of Medicine (NLM) in the ImageCLEF 2017 caption task. We proposed different machine learning methods using training subsets that we selected from the provided data as well as retrieval methods using external data. For the concept detection subtask, we used Convolutional Neural Networks (CNNs) and Binary Relevance using decision trees for multi-label classification. We also proposed a retrieval-based approach using Open-i image search engine and MetaMapLite to recognize relevant terms and associated Concept Unique Identifiers (CUIs). For the caption prediction subtask, we used the recognized CUIs and the UMLS to generate the captions. We also applied Open-i to retrieve similar images and their captions. We submitted ten runs for the concept detection subtask and six runs for the caption prediction subtask. CNNs provided good results with regards to the size of the selected subsets and the limited number of CUIs used for training. Using the CUIs recognized by the CNNs, our UMLS-based method for caption prediction obtained good results with 0.2247 mean BLUE score. In both subtasks, the best results were achieved using retrieval-based approaches outperforming all submitted runs by all the participants with 0.1718 mean F1 score in the concept detection subtask and 0.5634 mean BLUE score in the caption prediction subtask.
Duration, prevalence and intensity of bacteraemia after dental extractions in children

Objective: To investigate the duration, prevalence and intensity of bacteraemia after dental extractions in children by comparing within-patient bacteraemia before and after dental extraction. Methods: Children were randomly allocated to one of 10 postprocedure time groups from 10 s to 60 min. The differences between intensity and prevalence of the bacteraemia at each time after extractions were used to estimate the duration of the bacteraemia. After attainment of general anaesthesia, pre-extraction and postextraction blood samples were processed by broth culture and lysis filtration to isolate and quantify bacteria present in the patients’ blood. Results: 500 subjects between 3 and 16 years old were recruited. The estimated duration of bacteraemia was about 11 min. Conclusions: The duration of bacteraemia after dental extractions is less than previously thought. This has implications for the interpretation of odontogenic bacteraemia studies.
Competition between Core-2 GlcNAc-transferase and ST6GalNAc-transferase Regulates the Synthesis of the Leukocyte Selectin Ligand on Human P-selectin Glycoprotein Ligand-1*

Background: Carbohydrate epitopes at the N terminus of PSGL-1 (P-selectin glycoprotein ligand-1) facilitate leukocyte binding to selectins. Results: O-linked glycan microheterogeneity analysis at the PSGL-1 N terminus demonstrates the presence of both the core-2 sialyl Lewis-X (sLeX) and di-sialylated T-antigen. Conclusion: Overexpression of ST6GalNAc-transferases reduced both sLeX expression and selectin-mediated leukocyte adhesion. Significance: ST6GalNAc2 is a novel enzyme that regulates leukocyte adhesion under fluid shear. The binding of selectins to carbohydrate ligands expressed on leukocytes regulates immunity and inflammation. Among the human selectin ligands, the O-linked glycans at the N-terminus of the leukocyte cell-surface molecule P-selectin glycoprotein ligand-1 (PSGL-1, CD162) are important because they bind all selectins (L-, E-, and P-selectin) with high affinity under hydrodynamic shear conditions. Analysis of glycan microheterogeneity at this site is complicated by the presence of 72 additional potential O-linked glycosylation sites on this mucinous protein. To overcome this limitation, truncated forms of PSGL-1, called “PSGL-1 peptide probes,” were developed. Ultra-high sensitivity mass spectrometry analysis of glycans released from such probes along with glycoproteomic analysis demonstrate the presence of both the sialyl Lewis-X (sLeX) and the di-sialylated T-antigen (NeuAcα2,3Galβ1,3(NeuAcα2,6)GalNAc) at the PSGL-1 N-terminus. Overexpression of glycoprotein-specific ST6GalNAc-transferases (ST6GalNAc1, -2, or -4) in human promyelocytic HL-60 cells altered glycan structures and cell adhesion properties. In particular, ST6GalNAc2 overexpression abrogated cell surface HECA-452/CLA expression, reduced the number of rolling leukocytes on P- and L-selectin-bearing substrates by ∼85%, and increased median rolling velocity of remaining cells by 80–150%. Cell rolling on E-selectin was unaltered although the number of adherent cells was reduced by 60%. ST6GalNAc2 partially co-localizes in the Golgi with the core-2 β(1,6)GlcNAc-transferase C2GnT-1. Overall, the data describe the glycan microheterogeneity at the PSGL-1 N-terminus. They suggest that a competition between ST6GalNAc2 and C2GnT-1 for the core-1/Galβ1,3GalNAc glycan may regulate leukocyte adhesion under fluid shear.
Primary reactions of the LOV2 domain of phototropin, a plant blue-light photoreceptor.

The phototropins constitute an important class of plant photoreceptor kinases that control a range of physiological responses, including phototropism, light-directed chloroplast movement, and light-induced stomatal opening. The LOV2 domain of phototropin binds a molecule of flavin mononucleotide (FMN) and undergoes a photocycle involving light-driven covalent adduct formation between a conserved cysteine residue and the C(4a) atom of FMN. This product state promotes C-terminal kinase activation and downstream signal transduction. Here, we report the primary photophysics and photochemistry of LOV2 domains of phototropin 1 of Avena sativa (oat) and of the phy3 photoreceptor of Adiantum capillus-veneris (maidenhair fern). In agreement with earlier reports [Swartz, T. E. , et al. (2001) J. Biol. Chem. 276, 36493-36500], we find that the FMN triplet state is the reactive species from which the photoreaction occurs. We demonstrate that the triplet state is the primary photoproduct in the LOV2 photocycle, generated at 60% efficiency. No spectroscopically distinguishable intermediates precede the FMN triplet on the femtosecond to nanosecond time scale, indicating that it is formed directly via intersystem crossing (ISC) from the singlet state. Our results indicate that the majority of the FMN triplets in the LOV2 domain exist in the protonated form. We propose a reaction mechanism that involves excited-state proton transfer, on the nanosecond time scale or faster, from the sulfhydryl group of the conserved cysteine to the N5 atom of FMN. This event promotes adduct formation by increasing the electrophilicity of C(4a) and subsequent nucleophilic attack by the cysteine's thiolate anion. Comparison to free FMN in solution shows that the protein environment of LOV2 increases the ISC rate of FMN by a factor of 2.4, thus improving the yield of the cysteinyl-flavin adduct and the efficiency of phototropin-mediated signaling processes.
N‐acyl amines of docosahexaenoic acid and other n–3 polyunsatured fatty acids – from fishy endocannabinoids to potential leads

N–3 long‐chain polyunsaturated fatty acids (n–3 LC‐PUFAs), in particular α‐linolenic acid (18:3n‐3), eicosapentaenoic acid (EPA; 20:5n‐3) and docosahexaenoic acid (DHA; 22:6n‐3) are receiving much attention because of their presumed beneficial health effects. To explain these, a variety of mechanisms have been proposed, but their interactions with the endocannabinoid system have received relatively little attention so far. However, it has already been shown some time ago that consumption of n–3 LC‐PUFAs not only affects the synthesis of prototypic endocannabinoids like anandamide but also stimulates the formation of specific n–3 LC‐PUFA‐derived conjugates with ethanolamine, dopamine, serotonin or other amines. Some of these fatty amides show overlapping biological activities with those of typical endocannabinoids, whereas others possess distinct and sometimes largely unknown receptor affinities and other properties. The ethanolamine and dopamine conjugates of DHA have been the most investigated thus far. These mediators may provide promising new leads to the field of inflammatory and neurological disorders and for other pharmacological applications, including their use as carrier molecules for neurotransmitters to target the brain. Furthermore, combinations of n–3 LC‐PUFA‐derived fatty acid amides, their precursors and FAAH inhibitors offer possibilities to optimise their effects in health and disease.