Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunologic characterization of a cloned fragment containing the species-specific epitope from the major outer membrane protein of Chlamydia trachomatis

A 183-bp fragment encoding variable domain IV (VD IV) of Chlamydia trachomatis serovar B major outer membrane protein (MOMP) (amino acids 273 to 333) and containing the species-specific epitope was cloned and expressed in Escherichia coli as a fusion protein with Schistosoma japonicum glutathione S-transferase (GST-VD IV). The fusion protein was affinity purified under nondenaturing conditions and used to immunize rabbits. Antisera were characterized by microimmunofluorescence, immunoblot, dot blot, peptide enzyme-linked immunosorbent, and in vitro neutralization assays. Antisera recognized MOMP from all 12 tested serovars of C. trachomatis but not from Chlamydia psittaci. In a dot blot assay, antisera bound to elementary bodies of serovars B, D, E, L2, and K in a strong fashion and to elementary bodies of serovars F, G, A, and H in a weak fashion but not to elementary bodies of serovars C, J, and I. High-resolution peptide mapping with synthetic overlapping serovar B MOMP peptides in a solid-phase enzyme-linked immunosorbent assay showed that immunization with GST-VD IV produced a serologic response that closely mimicked the response produced with purified serovar B elementary bodies. Antipeptide antibodies with strong binding to species- and subspecies-specific epitopes were elicited. Antisera were able to neutralize only those C. trachomatis serovars that bound antibodies in the dot blot assay. These results suggest that antigenic fragments from VD IV containing the species-specific epitope may be useful in the construction of a chlamydial vaccine for some but not all C. trachomatis serovars.
Actopaxin (α-Parvin) Phosphorylation Is Required for Matrix Degradation and Cancer Cell Invasion*

Background: The process of matrix degradation is an integral component of cell invasion. Results: Actopaxin phosphorylation is required for matrix degradation. Conclusion: Actopaxin can act upstream of Rho GTPase signaling via an interaction with β-PIX and PAK to control matrix degradation. Significance: Matrix degradation is a pivotal step in cell invasion and cancer cell metastasis. Dysregulation of cell adhesion and motility is known to be an important factor in the development of tumor malignancy. Actopaxin (α-parvin) is a paxillin, integrin-linked kinase, and F-actin binding focal adhesion protein with several serine phosphorylation sites in the amino terminus that contribute to the regulation of cell spreading and migration. Here, phosphorylation of actopaxin is shown to contribute to the regulation of matrix degradation and cell invasion. Osteosarcoma cells stably expressing wild type (WT), nonphosphorylatable (Quint), and phosphomimetic (S4D/S8D) actopaxin demonstrate that actopaxin phosphorylation is necessary for efficient Src and matrix metalloproteinase-driven degradation of extracellular matrix. Rac1 was found to be required for actopaxin-induced matrix degradation whereas inhibition of myosin contractility promoted degradation in the phosphomutant-expressing Quint cells, indicating that a balance of Rho GTPase signaling and regulation of cellular tension are important for the process. Furthermore, actopaxin forms a complex with the Rac1/Cdc42 GEF β-PIX and Rac1/Cdc42 effector PAK1, to regulate actopaxin-dependent matrix degradation. Actopaxin phosphorylation is elevated in the invasive breast cancer cell line MDA-MB-231 compared with normal breast epithelial MCF10A cells. Expression of the nonphosphorylatable Quint actopaxin in MDA-MB-231 cells inhibits cell invasion whereas overexpression of WT actopaxin promotes invasion in MCF10A cells. Taken together, this study demonstrates a new role for actopaxin phosphorylation in matrix degradation and cell invasion via regulation of Rho GTPase signaling.
Introducing Variable Gap Penalties into Three-Sequence Alignment for Protein Sequences

The common-use gap penalty strategies, constant penalty and affine gap penalty, have been adopted in the traditional three-sequence alignment algorithm which considers the insertion, deletion and substitution. However, these strategies are not suitable to protein sequence alignments. For the alignment accuracy of protein sequences, the gap penalty is a major determinant. Incorporating protein structure information to vary the gap penalties can lead to more biologically correct alignments. Here, we present an algorithm to find a global and optimal alignment among three protein sequences by using position- specific gap penalties which allow gap penalties to be varied. Thus, residue-dependent information and protein structure information can be applied to the three-sequence alignment. The experimental results show that our algorithm achieves the significant improvement in the accuracy of alignments than the three-sequence alignment algorithm with the affine gap penalty for protein sequences.
Minocycline protects against delayed cerebral ischemia after subarachnoid hemorrhage via matrix metalloproteinase‐9 inhibition

Delayed cerebral ischemia (DCI) is an independent risk factor for poor outcome after aneurysmal subarachnoid hemorrhage (SAH) and is multifactorial in etiology. While prior studies have suggested a role for matrix metalloproteinase‐9 (MMP‐9) in early brain injury after SAH, its contribution to the pathophysiology of DCI is unclear.
Advance Information and Asset Prices

This paper provides a dynamic rational expectations equilibrium model in which investors have heterogeneous information and investment opportunities. Informed investors privately receive advance information about future earnings that is unrelated to current earnings. In response to good advance information, stock prices increase and informed investors act as trend chasers, increasing their investment in stocks. Informed investors also buy other investment opportunities that are positively correlated with stocks, bearing more aggregate risk. The expected risk premium increases generating short-run momentum. Uninformed investors sell stocks, acting as contrarians. When the advance information materializes in the future, excess returns fall, generating long-run reversals.
Muscle Contraction, but Not Insulin, Increases Microvascular Blood Volume in the Presence of Free Fatty Acid–Induced Insulin Resistance

OBJECTIVE Insulin and contraction each increase muscle microvascular blood volume (MBV) and glucose uptake. Inhibiting nitric oxide synthase blocks insulin's but not contraction's effects. We examined whether contraction could augment the MBV increase seen with physiologic hyperinsulinemia and whether free fatty acid (FFA)-induced insulin resistance differentially affects contraction- versus insulin-mediated increases in MBV. RESEARCH DESIGN AND METHODS Rats were fasted overnight. Plasma FFAs were increased by intralipid/heparin infusion (3 h), insulin was increased with a euglycemic clamp (3 mU · min−1 · kg−1), and hindlimb muscle contraction was electrically stimulated. Muscle MBV was measured using contrast-enhanced ultrasound. Insulin transport into muscle was measured using 125I-insulin. BQ-123 (0.4 mg/h) was used to block the endothelin-1 (ET-1) receptor A. RESULTS Superimposing contraction on physiologic hyperinsulinemia increased MBV within 10 min by 37 and 67% for 0.1 or 1 Hz, respectively (P < 0.01). FFA elevation alone did not affect MBV, whereas 0.1 Hz stimulation doubled MBV (P < 0.05) and increased muscle insulin uptake (P < 0.05) despite high FFA. Physiologic hyperinsulinemia during FFA elevation paradoxically decreased MBV (P < 0.05). This MBV decrease was reversed by either 0.1 Hz contraction or ET-1 receptor A antagonism, and the combination raised MBV above basal. CONCLUSIONS Contraction recruits microvasculature beyond that seen with physiologic hyperinsulinemia by a distinct mechanism that is not blocked by FFA-induced vascular insulin resistance. The paradoxical MBV decline seen with insulin plus FFA may result from differential inhibition of insulin-stimulated nitric oxide–dependent vasodilation relative to ET-1 vasoconstriction. Our results implicate ET-1 as a potential mediator of FFA-induced vascular insulin resistance.
Neocortical Synchronized Oscillations Induced by Thalamic Disinhibition In Vivo

Thalamocortical circuits are recognized as the main elements involved in the genesis of synchronized oscillations typical of certain generalized seizures. We addressed the capability of thalamic disinhibition to generate synchronized oscillations in neocortex. Microdialysis was used to infuse GABA(A) and GABA(B) receptor antagonists directly into the thalamus of anesthetized rats while recording cortical field potentials from 16 sites aligned perpendicular to the cortical surface, using 100 microm spaced linear array silicon probes. The results demonstrate that block of thalamic GABA(A) receptors induces continuous 3 Hz discharges in neocortex and that thalamic GABA(B) receptors mediate this activity. Also, during thalamic disinhibition sporadic long-lasting discharges at 12 Hz occur that do not depend on GABA(B) receptors. Current source density analysis of these activities revealed that the dynamics of sinks and sources for the 3 and 12 Hz discharges was quite distinct, in a way that suggests a different active involvement of the neocortex. The results indicate that intrathalamic inhibitory processes play an essential role in the generation of neocortical synchronized oscillatory activity that may be related to certain forms of generalized seizures.
Microwave Scanner-Sounder MTVZA-GY on New Russian Meteorological Satellite Meteor-M No. 2: Modeling, Calibration, and Measurements

On July 8, 2014 meteorological satellite “Meteor-M” no. 2 with a module of temperature and humidity atmospheric sensing MTVZA-GY was launched on a circular sun-synchronous orbit. Microwave radiometer MTVZA-GY has 16 imaging channels at frequencies of 10.65, 18.7, 23.8, 31.5, 36.5, 42.0, 48.0, and 91.65 GHz and 13 sounder channels at frequencies in the ranges of 52–57 and 176–191 GHz and carries out conical scanning of the Earth at the angle of incidence 65°. Swath width is 1500 km. The brightness temperatures TBs were computed by numerical integration of microwave radiative transfer equation using the radiosonde and reanalysis atmospheric profiles as the input information. The TBs for the Amazon forest and the calm Ocean under clear sky served for the vicarious calibration of MTVZA channels. The long-term stability of MTVZA-GY operation was examined by the analysis of time series of TBs measured over the test areas around the Eastern Antarctic Dome C station, Greenland GEOSummit station and Amazon rainforest. TBs time series obtained by the GCOM-W1 AMSR2 radiometer for the same test areas served as a reference and were used for a comparison with MTVZA-GY time series. Examples are given of the global MTVZA-GY measurements.
Who Says I Do: The Changing Context of Marriage and Health and Quality of Life for LGBT Older Adults

Purpose of the Study: Until recently, lesbian, gay, bisexual, and transgender (LGBT) adults were excluded from full participation in civil marriage. The purpose of this study is to examine how legal marriage and relationship status are associated with health-promoting and at-risk factors, health, and quality of life of LGBT adults aged 50 and older. Design and Methods: We utilized weighted survey data from Aging with Pride: National Health, Aging, and Sexuality/Gender Study (NHAS) participants who resided in states with legalized same-sex marriage in 2014 (N = 1,821). Multinomial logistic regression was conducted to examine differences by relationship status (legally married, unmarried partnered, single) in economic and social resources; LGBT contextual and identity factors; health; and quality of life. Results: We found 24% were legally married, and 26% unmarried partnered; one-half were single. Those legally married reported better quality of life and more economic and social resources than unmarried partnered; physical health indicators were similar between legally married and unmarried partnered. Those single reported poorer health and fewer resources than legally married and unmarried partnered. Among women, being legally married was associated with more LGBT microaggressions. Implications: LGBT older adults, and practitioners serving them, should become educated about how legal same-sex marriage interfaces with the context of LGBT older adults’ lives, and policies and protections related to age and sexual and gender identity. Longitudinal research is needed to understand factors contributing to decisions to marry, including short- and long-term economic, social, and health outcomes associated with legal marriage among LGBT older adults.
Art of Singular Vectors and Universal Adversarial Perturbations

Vulnerability of Deep Neural Networks (DNNs) to adversarial attacks has been attracting a lot of attention in recent studies. It has been shown that for many state of the art DNNs performing image classification there exist universal adversarial perturbations - image-agnostic perturbations mere addition of which to natural images with high probability leads to their misclassification. In this work we propose a new algorithm for constructing such universal perturbations. Our approach is based on computing the so-called (p, q)-singular vectors of the Jacobian matrices of hidden layers of a network. Resulting perturbations present interesting visual patterns, and by using only 64 images we were able to construct universal perturbations with more than 60 % fooling rate on the dataset consisting of 50000 images. We also investigate a correlation between the maximal singular value of the Jacobian matrix and the fooling rate of the corresponding singular vector, and show that the constructed perturbations generalize across networks.
Spontaneous network activity of cerebellar granule neurons: impairment by in vivo chronic cannabinoid administration

Synchronized activity of neuronal networks has been proposed to be essential for cerebellar function. To examine the occurrence and organization of spontaneous neuronal activity in the cerebellum in vivo, we imaged mouse cerebellar slices loaded with the intracellular Ca2+ concentration indicator, fura‐2. Recordings were then analysed statistically to identify correlated network activity. Ca2+ imaging revealed consistent spontaneous correlated network activity of granule cells (GC), which often occurred in clusters of coactivated GC. The number of spontaneously active GC, their activation frequency and correlation, were controlled by glutamate and GABA ionotropic receptors. These findings indicate that distinctive patterns of correlated activity between GC networks may be relevant for cerebellar circuit function. Cannabinoid antagonist‐precipitated Δ9‐tetrahydrocannabinol (THC) withdrawal impaired motor coordination. Given that the cerebellum has been suggested recently to be a main substrate for cannabinoid withdrawal, we used imaging of spontaneous network activity to examine whether GC, which contain CB1 cannabinoid receptors, respond to chronic THC treatment and withdrawal. Acute administration of THC had no effect on patterns of spontaneous GC network activity. In contrast, chronic THC administration severely impaired GC activity and network coordination. Incubation of cerebellar slices, from chronically THC‐treated mice, with the cannabinoid antagonist, SR141716A increased the number and network correlation of active GC. These data provide physiological evidence of the involvement of cerebellar circuits in the adaptive changes occurring during chronic THC exposure and withdrawal.
Increased glutamine in patients undergoing long-term treatment for schizophrenia: a proton magnetic resonance spectroscopy study at 3 T.

IMPORTANCE The N-methyl-d-aspartic acid receptor hypofunction model of schizophrenia predicts a paradoxical increase in synaptic glutamate release. In vivo measurement of glutamatergic neurotransmission in humans is challenging, but glutamine, the principal metabolite of synaptic glutamate, can be quantified with proton magnetic resonance spectroscopy (1H-MRS). Although a few studies have measured glutamate, glutamine, and glutamine to glutamate ratio, it is not clear which of these 1H-MRS indices of glutamatergic neurotransmission is altered in schizophrenia. OBJECTIVE To examine glutamine, glutamate, and glutamine to glutamate ratio in the dorsal anterior cingulate, as well as their relationships with symptoms and cognition in schizophrenia. DESIGN, SETTING, AND PARTICIPANTS Cross-sectional design using 3-T 1H-MRS in participants recruited from university-based psychiatric outpatient clinics who underwent neuroimaging at an affiliated research facility. Participants were 84 patients with a DSM-IV-TR diagnosis of schizophrenia and 81 psychiatrically healthy volunteers, matched in age, sex, ethnicity, and occupational level to the head of household of family of origin. MAIN OUTCOMES AND MEASURES Glutamine, glutamate, and glutamine to glutamate ratio. Also symptoms and cognition. RESULTS Glutamine was increased in the schizophrenia group (P = .01) as well as the glutamine to glutamate ratio (P = .007) but not glutamate (P = .89). Glutamine levels were positively correlated with severity of psychotic symptoms (P = .02). Choline was also increased in schizophrenia (P = .002). CONCLUSIONS AND RELEVANCE Elevated glutamine, which was directly related to psychotic symptoms, is consistent with increased glutamatergic synaptic release in schizophrenia, as predicted by the N-methyl-d-aspartic acid receptor hypofunction model. Further understanding the underlying mechanism of glutamatergic dysfunction in schizophrenia may lead to new pharmacological strategies to treat psychosis.
Squamous cell carcinoma in association with dental implants: an assessment of previously hypothesized carcinogenic mechanisms and a case report.

Although dental implants have seen tremendous clinical success over the past few decades, there are some worrying reports in literature describing squamous cell carcinoma (SCC) in close association with dental implants. This article also provides a critical assessment of the published literature relating to the presence of carcinoma in association with dental implants, analyzing the previously published and hypothesized carcinogenic responses to an implant, to try and come to a conclusion regarding the plausibility and clinical risk for cancer formation in association with dental implants. An unusual case of an SCC noted in close proximity to a dental implant is also presented. A systematic search was conducted using Medline (PubMed), Cochrane Database, and Google Scholar with the search terms "cancer," "squamous cell carcinoma," "dental implant," "SCC," "peri-implantitis," "oral cancer," and "implantology" and using multiple combinations using Boolean operators "or" and "and. " The search was not limited to dental literature; orthopedic and biomedical literature was also included. The results were then hand screened to pick out the relevant articles. In total, 14 previous published reports were found, where 24 dental implants were reported to be associated with SCC. Not all the reported patients had a history of cancer, but contributory factors such as smoking were found. An analysis of the biological plausibility of previously proposed carcinogenic mechanisms, such as corrosion, metallic ion release, and particulate debris, did not support the etiologic role for dental implants in cancer development, and the standardized incidence ratio was found to be extremely low (0.00017). Peri-implantitis should be assessed cautiously in patients receiving implants who have a previous history of cancer. Dental implants are a safe treatment modality based on the published data, and any change in surgical protocol is not mandated.
Evolving search spaces to emphasize the performance difference of real-coded crossovers using genetic programming

When we evaluate the search performance of an evolutionary computation (EC) technique, we usually apply it to typical benchmark functions and evaluate its performance in comparison to other techniques. In experiments on limited benchmark functions, it can be difficult to understand the features of each technique. In this paper, the search spaces that emphasize the performance difference of EC techniques are evolved by Cartesian genetic programming. We focus on a real-coded genetic algorithm, which is a type of genetic algorithm that has a real-valued vector as a chromosome. In particular, we generate search spaces using the performance difference of real-coded crossovers. In the experiments, we evolve the search spaces using the combination of three types of real-coded crossovers. As a result of our experiments, the search spaces that exhibit the largest performance difference of two crossovers are generated for all the combinations.
SPRINT: a brief global assessment of post-traumatic stress disorder

This report describes the reliability, validity, treatment sensitivity, diagnostic performance and normative values for the Short Post-Traumatic Stress Disorder (PTSD) Rating Interview (SPRINT), a brief, global assessment for PTSD. The SPRINT was administered to subjects participating in a clinical trial of PTSD and in a population survey assessing PTSD prevalence. The 8-item SPRINT includes questions assessing the core symptoms of PTSD, as well as related aspects of somatic malaise, stress vulnerability and functional impairment. Validity was assessed against the MINI structured interview, the Davidson Trauma Scale, Treatment Outcome for PTSD Scale, Connor-Davidson Resilience Scale, Sheehan Stress Vulnerability Scale, Sheehan Disability Scale and Clinical Global Impressions of Severity and Improvement Scales. Good test-retest reliability, internal consistency, convergent and divergent validity were obtained. The SPRINT was responsive to symptom change over time and correlated with comparable PTSD symptom measures. In victims of trauma, a score of 14-17 was associated with 96% diagnostic accuracy, whereas in those with PTSD, highest efficiency corresponded to a range of 11-13. The SPRINT demonstrates solid psychometric properties and can serve as a reliable, valid and homogeneous measure of PTSD illness severity and of global improvement.
Association between rheumatoid arthritis and psoriasis in total populations.

SummaryThe mathematical association between rheumatoid arthritis (classical, definite, probable, possible) and psoriasis (definite, probable) was investigated in total populations, 39,418 persons, in five geographical areas in Sweden. Rheumatoid arthritis was defined according to ARA-criteria, psoriasis according to special criteria (Hellgren, 67). The frequency of rheumatoid arthritis (classical, definite, probable) among 534 psoriatics (definite) was 5.4 % and among matched controls 0.9 %. Among males with definite and probable psoriasis, 7.6 % had rheumatoid arthritis of classical, definite, probable and possible type, and from these male psoriatics, 1.2 % had clinical typical arthritis psoriatica. Among females with definite and probable psoriasis, 9.1 % had rheumatoid arthritis (classical, definite, probable, possible) and from these female psoriatics, 1.1 % had clinical typical arthritis psoriatica. From all rheumatoid arthritics (classical, definite, probable) associated with psoriasis, males had i.