Miracle-dz/UniFAR-FTUs huggingface dataset:
Localization of Low-Density Detergent-Resistant Membrane Proteins in Intact and Acrosome-Reacted Mouse Sperm

Abstract Mammalian sperm become fertile after completing capacitation, a process associated with cholesterol loss and changes in the biophysical properties of the sperm membranes that prepares the sperm to undergo the acrosome reaction. Different laboratories have hypothesized that cholesterol efflux can influence the extent and/or movement of lipid raft microdomains. In a previous study, our laboratory investigated the identity of sperm proteins putatively associated with rafts. After extraction with Triton X-100 and ultracentrifugation in sucrose gradients, proteins distributing to the light buoyant-density fractions were cored from polyacrylamide gels and microsequenced. In this study, a subset of these proteins (TEX101, basigin, hexokinase 1, facilitated glucose transporter 3, IZUMO, and SPAM1) and other molecules known to be enriched in membrane rafts (caveolin 2, flotillin 1, flotillin 2, and the ganglioside GM3) were selected to investigate their localization in the sperm and their behavior during capacitation and the acrosome reaction. These molecules localize to multiple sperm domains, including the acrosomal cap (IZUMO, caveolin 2, and flotillin 2), equatorial segment (GM3), cytoplasmic droplet (TEX101), midpiece (basigin, facilitated glucose transporter 3, and flotillin 2), and principal piece (facilitated glucose transporter 3). Some of these markers modified their immunofluorescence pattern after sperm incubation under capacitating conditions, and these changes correlated with the occurrence of the acrosome reaction. While GM3 and caveolin 2 were not detected after the acrosome reaction, flotillin 2 was found in the equatorial segment of acrosome-reacted sperm, and IZUMO distributed along the sperm head, reaching the post- and para-acrosomal areas. Taking into consideration the requirement of the acrosome reaction for sperm to become fusogenic, these results suggest that membrane raft dynamics may have a role in sperm-egg membrane interaction.
Nonmetallic substrates for growth of silicene: an ab initio prediction

By means of first-principles calculations we predict the stability of silicene layers as buckled honeycomb lattices on Cl-passivated Si(1 1 1) and clean CaF2(1 1 1) surfaces. The van der Waals interaction between silicene and the inert substrate stabilizes the adsorbate system while not destroying the Si pz-derived linear bands forming Dirac cones at the Brillouin zone corners. Only small gaps of about 3 and 52 meV are opened.
Vitamin B12 deficiency neurological syndromes: a clinical, MRI and electrodiagnostic study.

BACKGROUND Vegetarianism is an important cause of vitamin B12 deficiency, especially in countries like India. We managed 17 patients with neurological syndrome due to vitamin B12 deficiency in a tertiary care referral teaching hospital which caters to relatively affluent population. AIM To evaluate neurophysiological and MRI changes in patients presenting with vitamin B12 deficiency neurological syndrome and interpret these is the light of reported autopsy findings. SETTING Tertiary care referral teaching hospital. METHODS Patients with vitamin B12 deficiency neurological syndrome diagnosed by low serum vitamin B12 and/or megaloblastic bone marrow were subjected to clinical evaluation and spinal MRI. The neurophysiological tests included nerve conduction studies, tibial somatosensory evoked potential (SEP), motor evoked potential (MEP) and visual evoked potential (VEP) studies. The recovery was defined on the basis of 6 months Barthel Index score into complete, partial or poor. RESULTS There were 17 patients with vitamin B12 deficiency neurological syndrome, 3 were females and 12 lactovegetarian. The clinical syndrome was that of myelopathy in 8, myeloneuropathy in 5, dementia myelopathy in 3 and neuropathy in 1 patient. All the patients had impaired joint position and vibration sensation in the lower limbs and 4 had in upper limbs as well. Lower limbs were spastic in 13 and upper limbs in 2 patients. Spinal MRI revealed T2 hyperintensity in cervicodorsal region in 6 and cord atrophy in 3 patients. Sural nerve conduction was abnormal in 8 and peroneal conduction in 5 patients. In one patient all sensory nerve conductions were unrecordable but motor conductions were normal. Tibial SEP was abnormal in 12 out of 15 and lower limb MEP in 8 out of 12 patients. P100 latency of VEP was prolonged in 7 out of 13 patients. Right to left asymmetry was present in tibial SEP in 4 and VEP in 2 patients. At 6 months followup 2 patients improved completely, 7 partially and 3 had poor recovery. Clinical recovery correlated with MEP but not with SEP or MRI changes. CONCLUSION The evoked potential and MRI changes in vitamin B12 deficiency neurological syndrome are consistent with focal demyelination of white matter in spinal cord and optic nerve. Myelopathic presentation is commoner and SEP is more frequently abnormal. The outcome at 6 months correlated with MEP changes.
Assessment of contamination by organochlorine pesticides in Solanum lycopersicum L. and Capsicum annuum L.: A market survey in Nigeria

This study investigated the presence and levels of organochlorine pesticides (OCPs) (hexachlorobenzene (HCB), α‑, β‑ ‑‑ ‑, δ‑, and γ‑hexachlorohexane (HCH), dieldrin, dichloro-diphenyltrichloroethane (p,p’-DDT), dichloro-diphenyl-dichloroethylene (p,p’-DDE), dichloro-diphenyldichloroethane (p,p’-DDD) and trans-nonachlor) in Solanum lycopersicum and Capsicum annuum samples commercially sold in Nigeria. OCPs were detected in all the samples analysed using HewlettPackard (HP 6890) gas chromatograph equipped with electron capture detector (GC-ECD). In S. lycopersicum, the total residue concentrations of ΣHCH (0.140 mg/kg), ΣHCB (0.144 mg/kg), ΣDDT (0.572 mg/kg), Σdieldrin (0.073 mg/kg), and Σtrans-nonachlor (0.117 mg/kg) were found. In C. annuum, the total residue levels of HCH, HCB, DDT, dieldrin and trans-nonachlor measured were 7.220, 0.096, 0.275, 0.037 and 0.117 mg/kg respectively. The α‑ ‑‑ ‑HCH isomer was not detected in S. lycopersicum and p,p’-DDD found only in C. annuum samples. The OCPs levels were generally below the FAOs maximum residue limits except for HCH and trans-nonachlor. A pair-wise linear correlations among concentrations of OCPs in S. lycopersicum samples indicated statistically significant (P = 0.05) relations between δ‑ ‑‑ ‑HCH and dieldrin (r = -0.997, P = 0.047), dieldrin and HCB (r = 0.99, P = 0.043), p,p’-DDD and p,p’-DDT (r = 1.00, P = 0.006).
Predictors of leisure-time physical activity among African American women.

OBJECTIVES To examine the extent to which social support and self-efficacy were related to the duration of leisure-time physical activity in a sample of African American women. METHODS Two hundred forty African American women completed a 45-item questionnaire at community health centers and churches. RESULTS Mean weekly physical activity was found to be 88 minutes. Self-efficacy (P < or = 0.01) and frequency of social support from friends (P < or = 0.01) were found to be significant predictors for physical activity and accounted for 23.7% of the variance. CONCLUSIONS Physical activity interventions for Black women must build on the constructs of self-efficacy and friends' social support.
Metastatic malignant disease to the parotid gland

A survey of over 250 consecutive parotidectornies performed at The Mason Clinic indicates a surprising incidence of metastatic malignant disease to the parotid gland. Four percent of all parotidectornies performed indicated a metastatic focus of malignancy from an unsuspected primary outside areas of the head and neck usually implicated in parotid disease. Twenty‐five percent of all cancer discovered at parotidectomy was metastatic malignant disease to the parotid gland. The most common site was the lung. A high index of suspicion, evaluation of pathologic specimens by electron microscopy, and detailed metastatic work‐up for patients with malignant disease in parotid lymph nodes are recommendations which should be considered by the surgeon performing parotid procedures.
Pen-2 Is Incorporated into the γ-Secretase Complex through Binding to Transmembrane Domain 4 of Presenilin 1*

γ-Secretase is a multimeric membrane protein complex comprised of presenilin (PS), nicastrin (Nct), Aph-1, and Pen-2. It is a member of an atypical class of aspartic proteases that hydrolyzes peptide bonds within the membrane. During the biosynthetic process of the γ-secretase complex, Nct and Aph-1 form a heterodimeric intermediate complex and bind to the C-terminal region of PS, serving as a stabilizing scaffold for the complex. Pen-2 is then recruited into this trimeric complex and triggers endoproteolysis of PS, conferring γ-secretase activity. Although the Pen-2 accumulation depends on PS, the binding partner of Pen-2 within the γ-secretase complex remains unknown. We reconstituted PS1 in Psen1/Psen2 deficient cells by expressing a series of PS1 mutants in which one of the N-terminal six transmembrane domains (TMDs) was swapped with those of CD4 (a type I transmembrane protein) or CLAC-P (a type II transmembrane protein). We report that the proximal two-thirds of TMD4 of PS1, including the conserved Trp-Asn-Phe sequence, are required for its interaction with Pen-2. Using a chimeric CD4 molecule harboring PS1 TMD4, we further demonstrate that the PS1 TMD4 bears a direct binding motif to Pen-2. Pen-2 may contribute to the activation of the γ-secretase complex by directly binding to the TMD4 of PS1.
Windows of opportunity for salt marsh vegetation establishment on bare tidal flats: The importance of temporal and spatial variability in hydrodynamic forcing

Understanding the mechanisms limiting and facilitating salt marsh vegetation initial establishment is of widespread importance due to the many valuable services salt marsh ecosystems offer. Salt marsh dynamics have been investigated by many previous studies, but the mechanisms that enable or disable salt marsh initial establishment are still understudied. Recently, the “windows of opportunity” (WoO) concept has been proposed as a framework providing an explanation for the initial establishment of biogeomorphic ecosystems and the role of physical disturbance herein. A WoO is a sufficiently long disturbance‐free period following seedling dispersal, which enables successful establishment. By quantifying the occurrence of WoO, vegetation establishment pattern can be predicted. For simplicity sake and as prove of concept, the original WoO framework considers tidal inundation as the only physical disturbance to salt marsh establishment, whereas the known disturbance from tidal currents and wind waves is ignored. In this study, we incorporate hydrodynamic forcing in the WoO framework. Its spatial and temporal variability is considered explicitly in a salt marsh establishment model. We used this model to explain the observed episodic salt marsh recruitment in the Westerschelde Estuary, Netherlands. Our results reveal that this model can significantly increase the spatial prediction accuracy of salt marsh establishment compared to a model that excludes the hydrodynamic disturbance. Using the better performing model, we further illustrate how tidal flat morphology determines salt marsh establishing elevation and width via hydrodynamic force distribution. Our model thus offers a valuable tool to understand and predict bottlenecks of salt marsh restoration and consequences of changing environmental conditions due to climate change.
Multimodal scale estimation for monocular visual odometry

Monocular visual odometry / SLAM requires the ability to deal with the scale ambiguity problem, or equivalently to transform the estimated unscaled poses into correctly scaled poses. While propagating the scale from frame to frame is possible, it is very prone to the scale drift effect. We address the problem of monocular scale estimation by proposing a multimodal mechanism of prediction, classification, and correction. Our scale correction scheme combines cues from both dense and sparse ground plane estimation; this makes the proposed method robust towards varying availability and distribution of trackable ground structure. Instead of optimizing the parameters of the ground plane related homography, we parametrize and optimize the underlying motion parameters directly. Furthermore, we employ classifiers to detect scale outliers based on various features (e.g. moments on residuals). We test our method on the challenging KITTI dataset and show that the proposed method is capable to provide scale estimates that are on par with current state-of-the-art monocular methods without using bundle adjustment or RANSAC.
A rountine diagnostic test for IgA and IgM antibodies to rubella virus: absorption of IgG with Staphylococcus aureus.

A simple method, in which IgG but not IgM or IgA antibodies were absorbed, was used for removal of long-standing antibodies to rubella virus; when specific immunoglobulins were left, a recent rubella infection was indicated. Staphylococcus aureus (heated and treated with formalin) was added to sera; the sera were then separated from staphylococci by centrifugation. Sera from women with a recent rubella infection or from women to whom live rubella vaccine had been
Surreptitious manipulation of the human host by Helicobacter pylori

Microbial pathogens contribute to the development of more than 1 million cases of cancer per year. Gastric adenocarcinoma is the second leading cause of cancer-related death in the world, and gastritis induced by Helicobacter pylori is the strongest known risk factor for this malignancy. H. pylori colonizes the stomach for years, not days or weeks, as is usually the case for bacterial pathogens and it always induces inflammation; however, only a fraction of colonized individuals ever develop disease. Identification of mechanisms through which H. pylori co-opts host defenses to facilitate its own persistence will not only improve diagnostic and therapeutic modalities, but may also provide insights into other diseases that arise within the context of long-term pathogen-initiated inflammatory states, such as chronic viral hepatitis and hepatocellular carcinoma.
Interpreting the evidence: choosing between randomised and non-randomised studies

This is the first of four articles Evaluations of healthcare interventions can either randomise subjects to comparison groups, or not. In both designs there are potential threats to validity, which can be external (the extent to which they are generalisable to all potential recipients) or internal (whether differences in observed effects can be attributed to differences in the intervention). Randomisation should ensure that comparison groups of sufficient size differ only in their exposure to the intervention concerned. However, some investigators have argued that randomised controlled trials (RCTs) tend to exclude, consciously or otherwise, some types of patient to whom results will subsequently be applied Furthermore, in unblinded trials the outcome of treatment may be influenced by practitioners' and patients' preferences for one or other intervention. Though non-randomised studies are less selective in terms of recruitment, they are subject to selection bias in allocation if treatment is related to initial prognosis. #### Summary points Treatment effects obtained from randomised and non-randomised studies may differ, but one method does not give a consistently greater effect than the other Treatment effects measured in each type of study best approximate when the exclusion criteria are the same and where potential prognostic factors are well understood and controlled for in the non-randomised studies Subjects excluded from randomised controlled trials tend to have a worse prognosis than those included, and this limits generalisability Subjects participating in randomised controlled trials evaluating treatment of existing conditions tend to be less affluent, educated, and healthy than those who do not; the opposite is true for trials of preventive interventions View this table: Threats to validity of evaluative research and possible solutions These issues have led to extensive debate, although empirical evidence is limited. This paper is a brief summary of a more detailed review1 of the impact of these potential threats. The review focused …
The Novel Human Coronaviruses NL63 and HKU1

In the mid-sixties of the previous century, the first two human coronaviruses (HCoV) were identified: HCoV-229E and HCoV-OC43 (29, 50, 70). These two human coronaviruses were studied extensively from approximately 1965 to the mid-1980s (7, 37, 49, 50, 57, 70). HCoV-229E is a member of the group I coronaviruses, and HCoV-OC43 is a member of group II. Besides the human coronaviruses, there are several group I and group II animal coronaviruses that infect cattle, pigs, cats, dogs, mice, and other animals (33). There is one additional branch, the group III coronaviruses, which are found exclusively in birds (33).
A Note on Unit Root Tests and GARCH Errors: A Simulation Experiment

This article re-examines the Monte Carlo experiments in Seo (1999) for unit root tests with GARCH errors. We report a Monte Carlo study with data generated from various GARCH(1, 1) processes where 0.8 ≤ α + β < 1 and β > α. In this case, the Dickey–Fuller test works better than the Seo test.
Direct projections from the anterior thalamic nuclei to the retrohippocampal region in the rat

The present study examined the areal and laminar distribution of direct projections from the anterior thalamic nuclei to the retrohippocampal region in the rat, with anterograde transport of Phaseolus vulgaris‐leucoagglutinin. The anteromedial nucleus (AM) projects to the temporal subiculum, medial entorhinal area, perirhinal area, and caudomedial part of the lateral entorhinal area. The interanteromedial nucleus (IAM) projects to the perirhinal area 0and the caudolateral part of the lateral entorhinal area. Furthermore, both the AM and IAM project to the temporal area 2, occipital area 1, and lateral occipital area 2. The projections from the AM and IAM to these retrohippocampal and neocortical regions terminate mainly in deep layers. The anteroventral nucleus (AV) projects to the subicular complex with a complex topographic organization. The most rostral part of the AV projects to layers I and III of the ventral presubiculum, the pyramidal cell layer of the temporal subiculum, and deep layers of the parasubiculum and medial entorhinal area. At the midrostrocaudal level of the AV, the lateral and the dorsal quadrants of the AV project, respectively, to layers I and III and to layers I and IV–VI of the ventral presubiculum, whereas the ventral and the medial quadrants project, respectively, to layers I and III and to layers I and IV–VI of the dorsal presubiculum. Furthermore, the lateral and dorsal quadrants project to the pyramidal cell layer of the temporal subiculum, whereas the ventral and medial quadrants project more septally. At the caudal third level of the AV, the dorsolateral part projects to layers I and III of the presubiculum with a patchy pattern and to the pyramidal cell layer of the septal subiculum. The anterodorsal nucleus projects mainly to deep layers of the presubiculum, parasubiculum, and entorhinal area. The results show that each subdivision of the anterior thalamic nuclei projects to a distinct field in the retrohippocampal region. This suggests that each of these projections may have a distinct modulatory influence upon the activity of retrohippocampal neurons that play important roles in limbic functioning such as memory and learning proceses. © 1993 Wiley‐Liss, Inc.
PROTEASOME PEPTIDASE ACTIVITIES PARALLEL HISTOMORPHOLOGICAL AND FUNCTIONAL CONSEQUENCES OF ISCHEMIA-REPERFUSION INJURY IN THE LUNG

Several lines of evidence suggest that the proteasome contributes to ischemia-reperfusion injury (I-RI) of organs. Although I-RI contributes to multiple disease processes in the lung, the regulation of proteasome activities during pulmonary I-RI is unknown. Thus, the authors performed a pilot study to define time-related changes of lung proteasome peptidase activities and to evaluate if possible alterations correspond to morphological and functional consequences of I-RI using a rat model. Animals underwent 120 minutes of unilateral lung ischemia. Ischemic and contralateral lungs were harvested at multiple time points for up to 168 hours of reperfusion (I-R30min-168h). Chymotryptic-like (CT-L) and tryptic-like (T-L) proteasome peptidase activities were measured in lung extracts. An early I-R–associated inactivation of proteasome activities paralleled impairment of oxygenation, edema formation, and degree of histopathology, and resolved with restoration of function within 24 to 72 hours. Although functional and histomorphological baseline conditions were still not fully achieved at I-R168h, proteasome activities increased continuously 1.4-fold (CT-L) and 5.7-fold (T-L) until I-R168h. Apparent KM values for the CT-L/T-L substrates were not influenced by I-R. This pilot study establishes an initial link between proteasome activities and physiological relevant consequences of lung I-RI, and further points towards a possible role of the proteasome during the postischemic tissue repair process.
Typical Frankia infect actinorhizal plants exotic to New Zealand

Abstract Frankia strains are actinomycetes that fix N2 in root nodules of plants classified in eight families of the Angiospermae. The wide variety of plants infected has raised questions about the ecology and diversity of Frankia symbionts, and their co-evolution with actinorhizal plants. Partial sequencing was done of the small subunit (16S) rRNA gene from Frankia endophytes present in the root nodules of Alnus cordata, A. glutinosa, A. viridis, Casuarina equisetifolia, Coriaria arborea, C. plumosa, and Elaeagnus pungens growing in New Zealand. With the exceptions of the Coriaria spp. , all of the plants are exotic to New Zealand. Analysis of the 16S rRNA gene indicates that the exotic species were nodulated by Frankia strains that cluster with strain groups previously shown to be typical for each actinorhizal host. Frankia in 12 native Coriaria spp. nodules yielded two sequences differing in only one position, suggesting a relatively low diversity compared with the exotic species.
Cloning and Expression of the Actinobacillus actinomycetemcomitans Thioredoxin (trx) Gene and Assessment of Cytokine Inhibitory Activity

ABSTRACT Thioredoxin is a ubiquitous redox control and cell stress protein. Unexpectedly, in recent years, thioredoxins have been found to exhibit both cytokine and chemokine activities, and there is increasing evidence that this class of protein plays a role in the pathogenesis of inflammatory diseases. In spite of this evidence, it has been reported that the oral bacterium and periodontopathogen Actinobacillus actinomycetemcomitans secretes an immunosuppressive factor (termed suppressive factor 1 [SF1] [T. Kurita-Ochiai and K. Ochiai, Infect. Immun. 64:50–54, 1996]) whose N-terminal sequence, we have determined, identifies it as thioredoxin. We have cloned and expressed the gene encoding the thioredoxin of A. actinomycetemcomitans and have purified the protein to homogeneity. The A. actinomycetemcomitans trx gene has 52 and 76% identities, respectively, to the trx genes ofEscherichia coli and Haemophilus influenzae. Enzymatic analysis revealed that the recombinant protein had the expected redox activity. When the recombinant thioredoxin was tested for its capacity to inhibit the production of cytokines by human peripheral blood mononuclear cells, it showed no significant inhibitory capacity. We therefore conclude that the thioredoxin of A. actinomycetemcomitans does not act as an immunosuppressive factor, at least with human leukocytes in cultures, and that the identity of SF1 remains to be elucidated.