Miracle-dz/UniFAR-FTUs huggingface dataset:
Localization of Carbonic Anhydrase XII to the Basolateral Membrane of H+-secreting Cells of Mouse and Rat Kidney

Membrane-associated carbonic anhydrase (CA) has a crucial role in renal HCO3 − absorption. CA activity has been localized to both luminal and basolateral membranes of the tubule epithelial cells. CA XII is a transmembrane isoenzyme that has been demonstrated in the basolateral plasma membrane of human renal, intestinal, and reproductive epithelia. The present study was designed to demonstrate the distribution of CA XII expression in the rodent kidney. A new polyclonal antibody to recombinant mouse CA XII was used in both Western blotting and immunohistochemistry. Western blotting analysis revealed a 40–45-kD polypeptide in CA XII-expressing CHO cells and isolated membranes of mouse and rat kidney. Immunofluorescence staining localized CA XII in the basolateral plasma membranes of S1 and S2 proximal tubule segments. Abundant basolateral staining of CA XII was seen in a subpopulation of cells in both cortical and medullary collecting ducts. Double immunofluorescence staining identified these cells as H+-secreting type A intercalated cells. The localization of CA XII in the peritubular space of proximal tubules suggests that it may play a role in renal HCO3 − absorption, whereas the function of CA XII in the type A intercalated cells needs further investigation.
Supervised and unsupervised methods for learning representations of linguistic units

Word representations, also called word embeddings, are generic representations, often high-dimensional vectors. They map the discrete space of words into a continuous vector space, which allows us to handle rare or even unseen events, e.g. by considering the nearest neighbors. Many Natural Language Processing tasks can be improved by word representations if we extend the task specific training data by the general knowledge incorporated in the word representations. The first publication investigates a supervised, graph-based method to create word representations. This method leads to a graph-theoretic similarity measure, CoSimRank, with equivalent formalizations that show CoSimRank’s close relationship to Personalized Page-Rank and SimRank. The new formalization is efficient because it can use the graph-based word representation to compute a single node similarity without having to compute the similarities of the entire graph. We also show how we can take advantage of fast matrix multiplication algorithms. In the second publication, we use existing unsupervised methods for word representation learning and combine these with semantic resources by learning representations for non-word objects like synsets and entities. We also investigate improved word representations which incorporate the semantic information from the resource. The method is flexible in that it can take any word representations as input and does not need an additional training corpus. A sparse tensor formalization guarantees efficiency and parallelizability. In the third publication, we introduce a method that learns an orthogonal transformation of the word representation space that focuses the information relevant for a task in an ultradense subspace of a dimensionality that is smaller by a factor of 100 than the original space. We use ultradense representations for a Lexicon Creation task in which words are annotated with three types of lexical information – sentiment, concreteness and frequency. The final publication introduces a new calculus for the interpretable ultradense subspaces, including polarity, concreteness, frequency and part-of-speech (POS). The calculus supports operations like “−1 × hate = love” and “give me a neutral word for greasy” (i.e., oleaginous) and extends existing analogy computations like “king − man + woman = queen”.
Image-based Open / Closed Eye Status Determination for Embedded System

In this paper, we propose a simple SVM, or support vector machine, classifier-based algorithm for determining whether eyes are open or closed in images. Due to its computational simplicity, it can be implemented on embedded systems, such as the Blackfin Low-Power Imaging Platform (BLIP) by Analog Devices, Inc. This design provides an inexpensive and practical solution to drowsiness detection functionality in applications such as assistive devices for vehicle drivers or machinery operators. Keywords—eye status; image processing; machine learning; classifier; drowsiness detection; embedded systems
Parent Involvement in School: English Speaking versus Spanish Speaking Families

The purpose of the present study was to explore the relationships between three predictor variables (attitude toward school, parent-child communication, and school commitment action) and the criterion variable (parent involvement) in a representative sample and to examine if these relationships were consistent across three groups (English speaking Caucasian family, English speaking Latino family, and Spanish speaking Latino families). Using a national database (N = 9.841), multi-group SEM analyses were conducted to investigate the relationship between three predictor variables and the criterion variable in three family groups. While all three predictor variables significantly predicted parent involvement in English speaking Caucasian and Latino families, only two variables (parent-child communication and school commitment actions), significantly predicted parent involvement in Spanish speaking Latino families. The results of this study suggest that when administrators, teachers and counselors in school strive to share specific school-related information with Latino families, Spanish speaking families are more likely to become involved with schools. El objetivo de este estudio fue evaluar las relaciones entre tres variables predictoras (actitud hacia la escuela, comunicación padres-hijos, y acciones de compromiso escolar) y una variable criterio (implicación de los padres) para examinar si esas relaciones eran consistentes en una muestra representativa de tres grupos (familias angloparlantes caucásicas, familias angloparlantes latinas, y familias hispanoparlantes latinas). Mediante una base de datos nacional (N = 9,841) y análisis multigrupo (SEM) se evaluó la relación entre las tres variables predictoras y la variable criterio en los tres tipos de familias. Los resultados indicaron que las variables predictoras eran un indicativo de la implicación de los padres en las familias angloparlantes caucásicas, y latinas, sólo dos de esas variables (comunicación padres-hijos y acciones de compromiso escolar) predecían la implicación de los padres en las familias hispanoparlantes. Asimismo, sugieren que cuando administradores, profesores y consejeros de la escuela se esfuerzan en compartir información específicamente relacionada con la escuela con familias latinas, los hispanohablantes muestran una mayor probabilidad a implicarse en todo el proceso educativo de sus hijos.
Rare Branched Fatty Acids Characterize the Lipid Composition of the Intra-Aerobic Methane Oxidizer “Candidatus Methylomirabilis oxyfera”

ABSTRACT The recently described bacterium “Candidatus Methylomirabilis oxyfera” couples the oxidation of the important greenhouse gas methane to the reduction of nitrite. The ecological significance of “Ca. Methylomirabilis oxyfera” is still underexplored, as our ability to identify the presence of this bacterium is thus far limited to DNA-based techniques. Here, we investigated the lipid composition of “Ca. Methylomirabilis oxyfera” to identify new, gene-independent biomarkers for the environmental detection of this bacterium. Multiple “Ca. Methylomirabilis oxyfera” enrichment cultures were investigated. In all cultures, the lipid profile was dominated up to 46% by the fatty acid (FA) 10-methylhexadecanoic acid (10MeC16:0). Furthermore, a unique FA was identified that has not been reported elsewhere: the monounsaturated 10-methylhexadecenoic acid with a double bond at the Δ7 position (10MeC16:1Δ7), which comprised up to 10% of the total FA profile. We propose that the typical branched fatty acids 10MeC16:0 and 10MeC16:1Δ7 are key and characteristic components of the lipid profile of “Ca. Methylomirabilis oxyfera. ” The successful detection of these fatty acids in a peatland from which one of the enrichment cultures originated supports the potential of these unique lipids as biomarkers for the process of nitrite-dependent methane oxidation in the environment.
Factors affecting insertion time and patient discomfort during colonoscopy.

BACKGROUND Successful colonoscopy depends on insertion of the instrument to the cecum, precise observation, and minimal patient discomfort during the procedure. The aim of this prospective study was to determine whether certain variables are associated with insertion time and patient discomfort during colonoscopy. METHODS Nine hundred nine consecutive colonoscopic examinations performed by a single endoscopist in patients without obstructive disease of the colorectum were analyzed. Four liters of Colonlyte (Taejun, Seoul, Korea) were used for bowel cleansing, and meperidine (25 mg) was administered intramuscularly 10 minutes before the procedure. The degree of patient discomfort was assessed using a 5-level Likert scale. RESULTS Among 909 study patients, colonoscopy was completed to the cecum in 876 patients (96.4%). The adjusted completion rate was 98% and mean insertion time for complete colonoscopy was 6.9+/-4.2 minutes. Colonoscopy caused less patient discomfort than barium enema or esophagogastroduodenoscopy. Multivariate logistic regression analysis demonstrated that inadequate bowel cleansing, advanced age, and constipation as an indication are independent factors associated with prolonged insertion time (>10 minutes). Female gender was the only independent factor associated with significant discomfort (> or = level 4) during colonoscopy. CONCLUSIONS Among the factors affecting insertion time and patient discomfort during colonoscopy, unsatisfactory bowel preparation was the only correctable factor.
A novel microfluidic design for blood plasma separation

one of the most crucial materials used in detection and diagnosis field is blood. The effects of blood components on the diagnosis process are significant. To avoid the disturbance of the experiments, the first step of blood analysis is to separate plasma from blood. Two dominant factors influence on this procedure are blood plasma skimming and Zweifach-Fung effect. In order to evaluate the separation device, two major criteria including separation and purity efficiency are introduced. The main drawback of these two factors is that they have reverse effect on each other which means that correcting one of them have destructive effect on the other one. Therefore, a trade-off between them should have happened. In this study, a novel microfluidic separation device is designed based on momentum definition and acceleration-deceleration effect. The computational CFD package, Ansys Fluent is used to simulate and solve this study. The Lagrangian approach is utilized for particle trajectory and the effect of the forces acting on each blood cell is considered. The results are then analyzed and shown that by using momentum and acceleration-deceleration effects, the purity efficiency would be increased by 15% with the same separation efficiency as before which was 70% on the average flow rate of 100 µl/min, approximately and it is completely providing for future use of this kind of device.
The PhyR‐σEcfG signalling cascade is involved in stress response and symbiotic efficiency in Bradyrhizobium japonicum

PhyR is an unusual type of response regulator consisting of a receiver domain and an extracytoplasmic function (ECF) sigma factor‐like domain. It was recently described as a master regulator of general stress response in Methylobacterium extorquens. Orthologues of this regulator are present in essentially all free‐living Alphaproteobacteria. In most of them, phyR is genetically closely linked to a gene encoding an ECF σ factor. Here, we investigate the role of these two regulators in the soybean symbiont Bradyrhizobium japonicum USDA110. Using deletion mutants and phenotypic assays, we showed that PhyR and the ECF σ factor σEcfG are involved in heat shock and desiccation resistance upon carbon starvation. Both mutants had symbiotic defects on the plant hosts Glycine max (soybean) and Vigna radiata (mungbean). They induced fewer nodules than the wild type and these nodules were smaller, less pigmented, and their specific nitrogenase activity was drastically reduced 2 or 3 weeks after inoculation. Four weeks after infection, soybean nodule development caught up to a large extent whereas most mungbean nodules remained defective even 5 weeks after infection. Remarkably, both mutants triggered aberrant nodules on the different host plants with ectopically emerging roots. Microarray analysis revealed that PhyR and σEcfG control congruent regulons suggesting both regulators are part of the same signalling cascade. This finding was further substantiated by in vitro protein–protein interaction studies which are in line with a partner‐switching mechanism controlling gene regulation triggered by phosphorylation of PhyR. The large number of genes of unknown function present in the PhyR/σEcfG regulon and the conspicuous symbiotic phenotype suggest that these regulators are involved in the Bradyrhizobium–legume interaction via yet undisclosed mechanisms.
Oogenesis in Xenopus laevis (Daudin). I. Stages of oocyte development in laboratory maintained animals

Oogenesis in the anuran Xenopus laevis can be divided into six stages based on the anatomy of the developing oocyte. Stage I consists of small (50 to 100 μ) colorless oocytes whose cytoplasm is transparent. Their large nuclei and mitochondrial masses are clearly visible in the intact oocyte. Stage II oocytes range up to 450 μ in diameter, and appear white and opaque. Stage I and II are both previtellogenic. Pigment synthesis and yolk accumulation (vitellogenesis) begins during Stage III. Vitellogenesis continues through Stage IV (600 to 1000 μ), the oocytes grow rapidly, and the animal and vegetal hemispheres become differentiated. By Stage V (1000 to 1200 μ) the oocytes have nearly reached their maximum size and yolk accumulation gradually ceases. Stage VI oocytes are characterized by the appearance of an essentially unpigmented equatorial band. They range in size from 1200 to 1300 μ, are postivtellogenic and ready for ovulation. These stages of oocyte development have been correlated with physiological and biochemical data related to oogenesis in Xenopus.
Two dimensional TV-L1 regularization for underwater acoustic source tracking

Bearing-time-record (BTR) is widely used in sonar signal processing as an important display formats which may benefit the subsequent processing. The general way to get a BTR display is to parallel the outputs of the beamformer along time axis. This paper proposes a method to generate the BTR display which uses the L1 norm regularization and the total variation (TV) regularization to enhance the point-based feature and the region-based feature respectively. To improve the clutter suppressing ability, the two-dimensional total variation is used, utilizing the the temporal continuities of the sources. The BTR display generated by the conventional beamforming (CBF), L1 regularization, one-dimensional (1D) TV-L1 regularization and two-dimensional (2D) TV-L1 regularization are compared through numeric simulations.
T-Cell Mediation of Pregnancy Analgesia Affecting Chronic Pain in Mice

It has been reported consistently that many female chronic pain sufferers have an attenuation of symptoms during pregnancy. Rats display increased pain tolerance during pregnancy due to an increase in opioid receptors in the spinal cord. Past studies did not consider the role of non-neuronal cells, which are now known to play an important role in chronic pain processing. Using an inflammatory (complete Freund's adjuvant) or neuropathic (spared nerve injury) model of persistent pain, we observed that young adult female mice in early pregnancy switch from a microglia-independent to a microglia-dependent pain hypersensitivity mechanism. During late pregnancy, female mice show no evidence of chronic pain whatsoever. This pregnancy-related analgesia is reversible by intrathecal administration of naloxone, suggesting an opioid-mediated mechanism; pharmacological and genetic data suggest the importance of δ-opioid receptors. We also observe that T-cell-deficient (nude and Rag1-null mutant) pregnant mice do not exhibit pregnancy analgesia, which can be rescued with the adoptive transfer of CD4+ or CD8+ T cells from late-pregnant wild-type mice. These results suggest that T cells are a mediator of the opioid analgesia exhibited during pregnancy. SIGNIFICANCE STATEMENT Chronic pain symptoms often subside during pregnancy. This pregnancy-related analgesia has been demonstrated for acute pain in rats. Here, we show that pregnancy analgesia can produce a complete cessation of chronic pain behaviors in mice. We show that the phenomenon is dependent on pregnancy hormones (estrogen and progesterone), δ-opioid receptors, and T cells of the adaptive immune system. These findings add to the recent but growing evidence of sex-specific T-cell involvement in chronic pain processing.
Assessing cognition and psychomotor function under long‐term treatment with controlled release oxycodone in non‐cancer pain patients

Background: The therapeutic use of opioids can be associated with altered cognition and impaired psychomotor function. Several studies have demonstrated the impact of opioid therapy on psychomotor performance and cognition, but no data exist about the effect of long‐term treatment with controlled release oxycodone (CRO) on driving ability.
Systematical design of X-ray FEL oscillator for the Shanghai coherent light facility

Shanghai Coherent Light Facility (SCLF) is a quasi-CW hard X-ray free electron laser user facility which is recently proposed. Due to the high repetition rate, high quality electron beams, it is straightforward to consider an X-ray free electron laser oscillator (XFELO) operation for SCLF. The main processes for XFELO design and optimization are proposed and major parameters required for the undulator, X-ray cavity and electron beam for XFELO operation are discussed. The first 3D X-ray crystal Bragg diffraction codes are built, which collaborates closely with GENESIS and OPC for numerical simulations of XFELO. Then performances of the expected fully coherent X-ray pulses are investigated and optimized by theoretical analysis and numerical simulation using new codes. The output pulse energy stability is studied analytically and the results are verified by simulation. Interestingly, the results display pulse energy oscillation in the low current mode XFELO, which is due to the “respiration” of pulse duration and the methods to reduce it in practice is proposed.
Development of an Ultrasonic Technique to Measure Specific Gravity in Lead-Acid Battery Electrolyte

An ultrasonic technique to measure specific gravity in lead- acid battery electrolyte is described in detail. This technique, which is based on the theory that the velocity of sound in a liquid depends on the density of the liquid, compares the ultrasonically measured velocity of sound in battery electrolyte (derived by measuring the time required for sound to traverse a known distance of electrolyte) to velocities in a computerstored data base relating velocity, density, and temperature. The experimental design, the data base developed for the method, a laboratory feasibility study, and an error analysis of the study are dis- cussed. The major advantages of the method are 1) the passive nature of the measurement, 2) the continuous sample and display capabilities, 3) the instantaneous tracking of changes in specific gravity, and 4) in- herent averaging of the specific gravity measurements.
An Analysis of Consumer Preferences for Information Sources on Food Safety by using Fuzzy Pair-wise Comparison

The main objective of this study is to measure consumer preferences for information sources on food safety along with the factors influencing the degree of consumer preferences in Turkey. The data were obtained from a survey of 385 consumers selected randomly in Izmir, Turkey. This study involves two-stage methodology. In the first stage, fuzzy pair-wise comparison was applied to calculate a measure of preferences. Five information sources on food safety, television programmes, doctors/experts, newspapers/journal articles, radio programmes and neighbors/friends were given to the consumers. The consumers were asked to make pair-wise comparisons among the information sources. The information source hierarchies of consumers were established and ranked from most to least importance. The results show that the most important information sources of consumers are “doctors/experts” and “television programmes”. The consumer preferences from the first stage were regressed upon the consumer specific variables by using seemingly unrelated regression in the second stage. The preferences for information sources are mainly influenced by education and level of income.
Bone marrow cells immunomagnetically selected for CD271+ antigen promote in vitro the repair of articular cartilage defects.

OBJECTIVE The purposes of this project were to quantify the cells expressing the mesenchymal stem cell (MSC) marker CD271 in synovial membranes from human osteoarthritic (OA) and healthy joints, and to determine if those CD271 cells were involved in spontaneous human cartilage repair and were beneficial for the repair of human articular cartilage defects. METHODS The coexpression of CD44/CD271, CD90/CD271, and CD105/CD271 antigens was determined by immunofluorescence in OA and healthy synovial membranes and during spontaneous cartilage repair. Isolated MSCs from the bone marrow of four OA patients (mean age: 64 years) were magnetically separated into MSC CD271+ and MSC CD271- subsets. The separated cell subsets were then implanted into 2 mm focal defects of articular cartilage. These implants were cultured in chondrogenic differentiation medium supplemented with recombinant human transforming growth factor-beta3 for 8 weeks. The repair tissues were analyzed by histochemistry (hematoxylin-eosin and safranin O) and immunohistochemistry for collage types I and II. RESULTS Cells expressing the CD271 antigen were diffusely distributed in OA synovial membranes and localized in the subintimal zone in healthy synovial membranes. The number of cells expressing MSC markers was higher in OA synovial membranes than in synovia from healthy joints, corresponding to the highest level of coexpression of CD90/CD271 antigens (9.8% vs. 2.6%). Spontaneous repair tissue showed more cells expressing the CD271 antigen (9.9% ± 4.0%). The highest levels of expression were found to be associated with CD44; 64% of positive CD271 cells coexpressed the CD44 antigen. In both implant cell types, the repair tissue morphology resembled articular cartilage, having an extracellular matrix with a hyaline aspect and numerous lacunae containing cells, and was immunopositive for collagen types I and II. Statistical analyses of the repair tissue demonstrated that the implantation of MSC CD271+ provided such benefits as a greater filling of the chondral defect and better integration between the repair tissue and native cartilage. Safranin O staining of repair tissue was negative in implants of MSC CD271- but more positive in implants with MSC CD271+. The overall histologic score for CD271- implants was 9.5 ± 0.89 and 12.19 ± 1.01 for CD271+ implants. CONCLUSIONS Synovial membranes from OA patients contain more cells expressing CD271 antigen than those from healthy joints, and spontaneous cartilage repair tissue contains cells positive for CD271 antigen. These data suggest the involvement of CD271 antigen in spontaneous cartilage repair and indicate that the cell subset MSC CD271+ provides higher quality chondral repair than the CD271- subset.