Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene expression related to serotonergic and glutamatergic neurotransmission is altered in the flinders sensitive line rat model of depression: Effect of ketamine

Major depressive disorder (MDD) is associated with dysfunctional serotonergic and glutamatergic neurotransmission, and the genetic animal model of depression Flinders Sensitive Line (FSL) rats display alterations in these systems relatively to their control strain Flinders Resistant Line (FRL). However, changes on transcript level related to serotonergic and glutamatergic signaling have only been sparsely studied in this model. The non‐competitive N‐methyl‐D‐aspartate (NMDA) receptor antagonist ketamine has fast‐onset antidepressant properties, and recent data implicate serotonergic neurotransmission in ketamine's antidepressant‐like activities in rodents. Here, we investigated the transcript levels of 40 genes involved in serotonergic and glutamatergic neurotransmission in FSL and FRL rats in response to a single dose of ketamine (15 mg/kg; 90 min prior to euthanization). Using real‐time quantitative polymerase chain reaction, we studied the effect of ketamine in the hippocampus, whereas strain differences were investigated in both hippocampus and frontal cortex. The expression of genes involved in serotonergic and glutamatergic neurotransmission were unaffected by a single dose of ketamine in the hippocampus. Relative to FRL rats, FSL rats displayed enhanced hippocampal transcript levels of 5‐ht2c, and P11, whereas the expression was reduced for 5‐ht2a, Nr2a, and Mglur2. In the frontal cortex, we found higher transcript levels of 5‐ht2c and Mglur2, whereas the expression of 5‐ht2a was reduced in FSL rats. Thus, ketamine is not associated with hippocampal alterations in serotonergic or glutamatergic genes at 90 min after an antidepressant dose. Furthermore, FSL rats display serotonergic and glutamatergic abnormalities on gene expression level that partly may resemble findings in MDD patients.
Survival Outcomes and Patterns of Recurrence in Patients with Stage III or IV Oropharyngeal Cancer Treated with Primary Surgery or Radiotherapy

Purpose To compare and contrast the patterns of failure in patients with locally advanced squamous cell oropharyngeal cancers undergoing curative-intent treatment with primary surgery or radiotherapy +/- chemotherapy. Methods and materials Two hundred and thirty-three patients with stage III or IV oropharyngeal squamous cell carcinoma who underwent curative-intent treatment from 2006-2012, were reviewed. The median length of follow-up for patients still alive at the time of analysis was 4.4 years. Data was collected retrospectively from a chart review. Results One hundred and thirty-nine patients underwent primary surgery +/- adjuvant therapy, and 94 patients underwent primary radiotherapy +/- chemotherapy (CRT). Demographics were similar between the two groups, except primary radiotherapy patients had a higher age-adjusted Charleston co-morbidity score (CCI). Twenty-nine patients from the surgery group recurred; 15 failed distantly only, seven failed locoregionally, and seven failed both distantly and locoregionally. Twelve patients recurred who underwent chemoradiotherapy; ten distantly alone, and two locoregionally. One patient who underwent radiotherapy (RT) alone failed distantly. Two and five-year recurrence-free survival rates for patients undergoing primary RT were 86.6% and 84.9% respectively. Two and five-year recurrence-free survival rates for primary surgery was 80.9% and 76.3% respectively (p=0.21). There was no significant difference in either treatment when they were stratified by p16 status or smoking status. Conclusions Our analysis does not show any difference in outcomes for patients treated with primary surgery or radiotherapy. Although the primary pattern of failure in both groups was distant metastatic disease, some local failures may be preventable with careful delineation of target volumes, especially near the base of skull region.
Cognitive neuropsychological analysis of differential reading and spelling disorder mechanisms in a patient with aphasia

ABSTRACT The purpose of this study was to determine if differential reading and spelling mechanisms were involved in a Japanese patient with aphasia. In our case, the patient scored low on all of the administered reading tasks, suggesting that both the reading lexical and non-lexical routes were impaired. In contrast, his writing-to-dictation score for Kana nonwords was high, suggesting that the spelling non-lexical route was intact. However, the patient scored low on a writing-to-dictation task comprised of high-familiarity Kanji words. The spelling lexical route was thought to be impaired. Therefore, the mechanism(s) involved in reading and spelling may differ in this case.
Guest Editor: B. O. Popescu Blood markers of oxidative stress in Alzheimer’s disease

Alzheimer′s disease (AD) represents a highly common form of dementia, but can be diagnosed in the earlier stages before dementia onset. Early diagnosis is crucial for successful therapeutic intervention. The introduction of new diagnostic biomarkers for AD is aimed at detecting underlying brain pathology. These biomarkers reflect structural or biochemical changes related to AD. Examination of cerebrospinal fluid has many drawbacks; therefore, the search for sensitive and specific blood markers is ongoing. Investigation is mainly focused on upstream processes, among which oxidative stress in the brain is of particular interest. Products of oxidative stress may diffuse into the blood and evaluating them can contribute to diagnosis of AD. However, results of blood oxidative stress markers are not consistent among various studies, as documented in this review. To find a specific biochemical marker for AD, we should concentrate on specific metabolic products formed in the brain. Specific fluorescent intermediates of brain lipid peroxidation may represent such candidates as the composition of brain phospholipids is unique. They are small lipophilic molecules and can diffuse into the blood stream, where they can then be detected. We propose that these fluorescent products are potential candidates for blood biomarkers of AD.
Unlikely Nomads: Settlement, Establishment, and Dislodgement Processes of Vegetative Seagrass Fragments

The dispersal of seagrasses is important to promoting the resilience and long-term survival of populations. Most of the research on long-distance dispersal to date has focused on sexual propagules while the dispersal of vegetative fragments has been largely overlooked, despite the important role this mechanism might play. In this study, we proposed a conceptual model that categorizes vegetative fragment dispersal into seven fundamental steps: i.e., (i) fragment formation, (ii) transport, (iii) decay, (iv) substrate contact, (v) settlement, (vi) establishment, and (vii) dislodgement. We present two experiments focusing on the final steps of the model from substrate contact to dislodgement in four tropical seagrass species (Cymodocea rotundata, Halophila ovalis, Halodule uninervis, and Thalassia hemprichii), which are critical for dispersed vegetative fragments to colonize new areas. We first conducted a mesocosm experiment to investigate the effect of fragment age and species on settlement (i.e., remains on the substrate in a rising tide) and subsequently establishment (i.e., rooting in substrate) rates. To determine dislodgement resistance of settled fragments, we also subjected fragments under different burial treatments to wave and currents in a flume. We found that both initial settlement and subsequent establishment rates increased with fragment age. H. ovalis was the only species that successfully established within the study period. After settlement, dislodgement resistance depended primarily on burial conditions. Smaller species H. ovalis and H. uninervis were also able to settle more successfully, and withstand higher bed shear stress before being dislodged, compared to the larger species T. hemprichii and C. rotundata. However, the ordinal logistic regressions did not reveal relationships between the tested plant morphometrics and the energy needed for dislodgement (with the exception of C. rotundata), indicating that there are potentially some untested species-specific traits that enable certain species to withstand dislodgement better. We discuss the implication our findings have on the dispersal potential for different species and the conservation of seagrasses. This study represents the first effort toward generating parameters for a bio-physical model to predict vegetative fragment dispersal.
Characteristics of the Epididymal Luminal Environment Responsible for Sperm Maturation and Storage

The testicular spermatozoa of all mammalian species are considered functionally immature owing to their inability to swim in a progressive manner and engage in productive interactions with the cumulus–oocyte complex. The ability to express these key functional attributes develops progressively during the cells’ descent through the epididymis, a highly specialized ductal system that forms an integral part of the male reproductive tract. The functional maturation of the spermatozoon is achieved via continuous interactions with the epididymal luminal microenvironment and remarkably, occurs in the complete absence of de novo gene transcription or protein translation. Compositional analysis of the luminal fluids collected from the epididymis of a variety of species has revealed the complexity of this milieu, with a diversity of inorganic ions, proteins, and small non-coding RNA transcripts having been identified to date. Notably, both the quantitative and qualitative profile of each of these different luminal elements display substantial segment-to-segment variation, which in turn contribute to the regionalized functionality of this long tubule. Thus, spermatozoa acquire functional maturity in the proximal segments before being stored in a quiescent state in the distal segment in preparation for ejaculation. Such marked division of labor is achieved via the combined secretory and absorptive activity of the epithelial cells lining each segment. Here, we review our current understanding of the molecular mechanisms that exert influence over the unique intraluminal environment of the epididymis, with a particular focus on vesicle-dependent mechanisms that facilitate intercellular communication between the epididymal soma and maturing sperm cell population.
Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns

Ringbauer et al. introduce a novel method to estimate barriers to gene flow in a two-dimensional population. Their inference scheme utilizes geographically. In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes than geographically well-separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that uses this signal to detect and estimate the strength of a linear barrier to gene flow in two dimensions. We use a diffusion approximation to model the effects of a barrier on the geographic spread of ancestry backward in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographic covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to an Antirrhinum majus (snapdragon) flower-color hybrid zone, where we do not detect any signal of a strong genome-wide barrier to gene flow.
Design and evaluation of a modular resonant switched capacitors equalizer for PV panels

A switched-capacitor based equalization scheme is proposed for overcoming the adverse effect of shaded panels in a serially connected PV array. The proposed solution is based on a modular approach, in which each two panels are connected to a resonant switched-capacitor converter. The distribution of currents and power extraction improvement have been derived and verified experimentally and design guidelines to meet desired power loss level requirements have been developed. The experimental equalizing module was designed for 185W PV panels and was found to boost the maximum available power by about 50% when interfaced with two serially connected PV panels under insolation ratios between 20% and 100%. The analytical, simulation and experimental results suggest that the proposed approach is effective in extracting all available power with relatively high efficiency.
Assay of the Multiple Energy-Producing Pathways of Mammalian Cells

Background To elucidate metabolic changes that occur in diabetes, obesity, and cancer, it is important to understand cellular energy metabolism pathways and their alterations in various cells. Methodology and Principal Findings Here we describe a technology for simultaneous assessment of cellular energy metabolism pathways. The technology employs a redox dye chemistry specifically coupled to catabolic energy-producing pathways. Using this colorimetric assay, we show that human cancer cell lines from different organ tissues produce distinct profiles of metabolic activity. Further, we show that murine white and brown adipocyte cell lines produce profiles that are distinct from each other as well as from precursor cells undergoing differentiation. Conclusions This technology can be employed as a fundamental tool in genotype-phenotype studies to determine changes in cells from shared lineages due to differentiation or mutation.
Interferon α2 and interferon γ induce the degranulation independent production of VEGF‐A and IL‐1 receptor antagonist and other mediators from human mast cells

Mast cells are resident immune effector cells, often studied in the context of allergic disease. Found in substantial numbers at sites of potential infection they are increased at sites of angiogenesis and can be pivotal for the sensing and clearance of a variety of pathogens. Interferons (IFNs) are cytokines that are critical for host defence against intracellular pathogens. Increased levels of IFNs are observed during viral infection and in autoimmune diseases. IFNs are also widely used therapeutically and have been examined in the therapy of severe asthma.
Ependymomas overexpress chemoresistance and DNA repair-related proteins

Background After surgery and radiation, treatment options for ependymoma are few making recurrence a challenging issue. Specifically, the efficacy of chemotherapy at recurrence is limited. We performed molecular profiling on a cohort of ependymoma cases in order to uncover therapeutic targets and to elucidate the molecular mechanisms contributing to treatment resistance. Results This ependymoma cohort showed minimal alterations in gene amplifications and mutations but had high expression rates of DNA synthesis and repair enzymes such as RRM1 (47%), ERCC1 (48%), TOPO1 (62%) and class III β-tublin (TUBB3) (57%), which are also all associated with chemoresistance. This cohort also had high expression rates of transporter proteins that mediate multi-drug resistance including BCRP (71%) and MRP1 (43%). Subgroup analyses showed that cranial ependymomas expressed the DNA synthesis enzyme TS significantly more frequently than spinal lesions did (57% versus 15%; p = 0.0328) and that increased TS expression was correlated with increased tumor grade (p = 0.0009). High-grade lesions were also significantly associated with elevated expression of TOP2A (p = 0.0092) and TUBB3 (p = 0.0157). Materials and Methods We reviewed the characteristics of 41 ependymomas (21 cranial, 20 spinal; 8 grade I, 11 grade II, 22 grade III) that underwent multiplatform profiling with immunohistochemistry, next-generation sequencing, and in situ hybridization. Conclusions Ependymomas are enriched with proteins involved in chemoresistance and in DNA synthesis and repair, which is consistent with the meager clinical effectiveness of conventional systemic therapy in ependymoma. Adjuvant therapies that combine conventional chemotherapy with the inhibition of chemoresistance-related proteins may represent a novel treatment paradigm for this difficult disease.
In vitro cytochrome P450 46A1 (CYP46A1) activation by neuroactive compounds

Cytochrome P450 46A1 (CYP46A1, cholesterol 24-hydroxylase) is the enzyme responsible for the majority of cholesterol elimination from the brain. Previously, we found that the anti-HIV drug efavirenz (EFV) can pharmacologically activate CYP46A1 in mice. Herein, we investigated whether CYP46A1 could also be activated by endogenous compounds, including major neurotransmitters. In vitro experiments with purified recombinant CYP46A1 indicated that CYP46A1 is activated by l-glutamate (l-Glu), l-aspartate, γ-aminobutyric acid, and acetylcholine, with l-Glu eliciting the highest increase (3-fold) in CYP46A1-mediated cholesterol 24-hydroxylation. We also found that l-Glu and other activating neurotransmitters bind to the same site on the CYP46A1 surface, which differs from the EFV-binding site. The other principal differences between EFV and l-Glu in CYP46A1 activation include an apparent lack of l-Glu binding to the P450 active site and different pathways of signal transduction from the allosteric site to the active site. EFV and l-Glu similarly increased the CYP46A1 kcat, the rate of the “fast” phase of the enzyme reduction by the redox partner NADPH–cytochrome P450 oxidoreductase, and the amount of P450 reduced. Spectral titrations with cholesterol, in the presence of EFV or l-Glu, suggest that water displacement from the heme iron can be affected in activator-bound CYP46A1. Moreover, EFV and l-Glu synergistically activated CYP46A1. Collectively, our in vitro data, along with those from previous cell culture and in vivo studies by others, suggest that l-Glu-induced CYP46A1 activation is of physiological relevance.
Ex vivo expansion of alveolar macrophages with Mycobacterium tuberculosis from the resected lungs of patients with pulmonary tuberculosis

Tuberculosis (TB), with the Mycobacterium tuberculosis (Mtb) as the causative agent, remains to be a serious world health problem. Traditional methods used for the study of Mtb in the lungs of TB patients do not provide information about the number and functional status of Mtb, especially if Mtb are located in alveolar macrophages. We have developed a technique to produce ex vivo cultures of cells from different parts of lung tissues surgically removed from patients with pulmonary TB and compared data on the number of cells with Mtb inferred by the proposed technique to the results of bacteriological and histological analyses used for examination of the resected lungs. The ex vivo cultures of cells obtained from the resected lungs of all patients were largely composed of CD14-positive alveolar macrophages, foamy or not, with or without Mtb. Lymphocytes, fibroblasts, neutrophils, and multinucleate Langhans giant cells were also observed. We found alveolar macrophages with Mtb in the ex vivo cultures of cells from the resected lungs of even those TB patients, whose sputum smears and lung tissues did not contain acid-fast Mtb or reveal growing Mtb colonies on dense medium. The detection of alveolar macrophages with Mtb in ex vivo culture as soon as 16–18 h after isolation of cells from the resected lungs of all TB patients suggests that the technique proposed for assessing the level of infection in alveolar macrophages of TB patients has higher sensitivity than do prolonged bacteriological or pathomorphological methods. The proposed technique allowed us to rapidly (in two days after surgery) determine the level of infection with Mtb in the cells of the resected lungs of TB patients and, by the presence or absence of Mtb colonies, including those with cording morphology, the functional status of the TB agent at the time of surgery.
The Combined Association of Modifiable Risk Factors with Breast Cancer Risk in the Women's Health Initiative

Although several modifiable risk factors have been independently associated with risk of breast cancer, few studies have investigated their joint association with breast cancer risk. Using a healthy lifestyle index (HLI) score, we assessed the association of a combination of selected modifiable risk factors (diet, alcohol, physical activity, BMI, and smoking) with risk of invasive breast cancer in the Women's Health Initiative (WHI). This study comprised 131,833 postmenopausal women, of whom 8,168 had breast cancer, who were enrolled in the WHI Observational Study or the WHI clinical trials. Cox proportional hazards regression was used to estimate the HRs and 95% confidence intervals (CI) for the association of the score with the risk of developing breast cancer overall and according to specific breast cancer clinicopathologic characteristics. There was a 4% reduction in the risk of breast cancer per unit increase in the HLI score. Compared with those with an HLI score in the lowest quintile level, those in the highest quintile level had 30%, 37%, and 30% lower risk for overall, ER+/PR+, and HER2+ breast cancer, respectively (HR = 0.70; 95% CI, 0.64–0.76; 0.63, 0.57–0.69; and 0.70; 0.55–0.90, respectively). We also observed inverse associations between the score and risk of breast cancer irrespective of nodal status, tumor grade, and stage of the disease. Most individual lifestyle factors were independently associated with the risk of breast cancer. Our findings support the view that promoting healthy lifestyle practices may be beneficial with respect to lowering risk of breast cancer among postmenopausal women. Cancer Prev Res; 11(6); 317–26. ©2018 AACR. See related editorial by Friedenreich and McTiernan, p. 313
A critical reappraisal of treatment response criteria in systemic mastocytosis and a proposal for revisions

Mast cell disease (MCD) is a hematopoietic stem cell neoplasm that is associated with infiltration of one or more organs with cytologically abnormal mast cells (MC). MCD is frequently but not always associated with a KIT mutation and, in some cases, is associated with clonal expansion of non‐MC lineage cells. In adults, there is almost always MC infiltration of the bone marrow, which is a cardinal feature of systemic mastocytosis (SM). While, as members of the wider community of physician scientists, we recognize the contribution of the current consensus treatment response criteria for SM, as individuals with more than average clinical experience in SM, we would like to point out their limitations and engage in a constructive discussion that will hopefully lead to a consideration for revisions. We present here an alternative proposal for treatment response assessments we believe is more objective, reproducible, and importantly, SM‐subtype specific, given the recent progress in our understanding of the natural history of this disease. We believe this proposal is timely given the prospects for new clinical trials in SM, and the related regulatory aspects of new drug approval that are currently not adequately addressed. The intent of this exercise is not to undermine the complexity of the disease or previous work by other investigators, but to come up with ideas for response criteria that are more practical and consider meaningful patient outcome.