Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep-structured hidden conditional random fields for phonetic recognition

We extend our earlier work on deep-structured conditional random field (DCRF) and develop deep-structured hidden conditional random field (DHCRF). We investigate the use of this new sequential deep-learning model for phonetic recognition. DHCRF is a hierarchical model in which the final layer is a hidden conditional random field (HCRF) and the intermediate layers are zero-th-order conditional random fields (CRFs). Parameter estimation and sequence inference in the DHCRF are developed in this work. They are carried out layer by layer so that the time complexity is linear to the number of layers. In the DHCRF, the training label is available only at the final layer and the state boundary is unknown. This difficulty is addressed by using unsupervised learning for the intermediate layers and lattice-based supervised learning for the final layer. Experiments on the standard TIMIT phone recognition task show small performance improvement of a three-layer DHCRF over a two-layer DHCRF; both are significantly better than the single-layer DHCRF and are superior to the discriminatively trained tri-phone hidden Markov model (HMM) using identical input features.
Both Canonical and Non-Canonical Wnt Signaling Independently Promote Stem Cell Growth in Mammospheres

The characterization of mammary stem cells, and signals that regulate their behavior, is of central importance in understanding developmental changes in the mammary gland and possibly for targeting stem-like cells in breast cancer. The canonical Wnt/β-catenin pathway is a signaling mechanism associated with maintenance of self-renewing stem cells in many tissues, including mammary epithelium, and can be oncogenic when deregulated. Wnt1 and Wnt3a are examples of ligands that activate the canonical pathway. Other Wnt ligands, such as Wnt5a, typically signal via non-canonical, β-catenin-independent, pathways that in some cases can antagonize canonical signaling. Since the role of non-canonical Wnt signaling in stem cell regulation is not well characterized, we set out to investigate this using mammosphere formation assays that reflect and quantify stem cell properties. Ex vivo mammosphere cultures were established from both wild-type and Wnt1 transgenic mice and were analyzed in response to manipulation of both canonical and non-canonical Wnt signaling. An increased level of mammosphere formation was observed in cultures derived from MMTV-Wnt1 versus wild-type animals, and this was blocked by treatment with Dkk1, a selective inhibitor of canonical Wnt signaling. Consistent with this, we found that a single dose of recombinant Wnt3a was sufficient to increase mammosphere formation in wild-type cultures. Surprisingly, we found that Wnt5a also increased mammosphere formation in these assays. We confirmed that this was not caused by an increase in canonical Wnt/β-catenin signaling but was instead mediated by non-canonical Wnt signals requiring the receptor tyrosine kinase Ror2 and activity of the Jun N-terminal kinase, JNK. We conclude that both canonical and non-canonical Wnt signals have positive effects promoting stem cell activity in mammosphere assays and that they do so via independent signaling mechanisms.
Comparison of Intravenous or Epidural Patient-controlled Analgesia in the Elderly after Major Abdominal Surgery

Background Patient-controlled analgesia (PCA) with intravenous morphine and patient-controlled epidural analgesia (PCEA), using an opioid either alone or in combination with a local anesthetic, are two major advances in the management of pain after major surgery. However, these techniques have been evaluated poorly in elderly people. This prospective, randomized study compared the effectiveness on postoperative pain and safety of PCEA and PCA after major abdominal surgery in the elderly patient. Methods Seventy patients older than 70 yr of age and undergoing major abdominal surgery were assigned randomly to receive either combined epidural analgesia and general anesthesia followed by postoperative PCEA, using a mixture of 0.125% bupivacaine and sufentanil (PCEA group), or general anesthesia followed by PCA with intravenous morphine (PCA group). Pain intensity was tested three times daily using a visual analog scale. Postoperative evaluation included mental status, cardiorespiratory and gastrointestinal functions, and patient satisfaction scores. Results Pain relief was better at rest (P = 0.001) and after coughing (P = 0.002) in the PCEA group during the 5 postoperative days. Satisfaction scores were better in the PCEA group. Although incidence of delirium was comparable in the PCA and PCEA groups (24%vs. 26%, respectively), mental status was improved on the fourth and fifth postoperative days in the PCEA group. The PCEA group recovered bowel function more quickly than did the PCA group. Cardiopulmonary complications were similar in the two groups. Conclusion After major abdominal surgery in the elderly patient, patient-controlled analgesia, regardless of the route (epidural or parenteral), is effective. The epidural route using local anesthetics and an opioid provides better pain relief and improves mental status and bowel activity.
The Endocrine Glands

A gland is an organ which takes something from the blood or other circulating mediunm and manufactures therefrom a secretioni which it delivers to the body as needed. Roughly there are two kinds of glands: those which deliver their secretion through ducts or tubes and those whose secretion is picked up directly bv the blood or lymph as it eirculates through the gland. The latter are know as ductless or endocrine glands. There are about a dozen of these in the human body. References to the endocrine glands and their disorders now appear in popular literature so frequently that it seems likely the well-informed person will shortly wish to have some accurate information regarding them. In the following paragraphs each of these glands is briefly discussed. They are arranged in the order of the frequency with which their disorders are encountered by the doctor. The PITUITARY is located in a sort of bony bubble on the floor of the cranial eavity between the temples and just back of the root of the nose. It is roughly divided into three parts which have different embryological origins. The front part, or anterior lobe, is pushed upward from the part of the embryo which later becomes the pharynx. The posterior lobe, or hind part, pushes downward from the floor of the brain. There is a stein which connects it with the brain. The anterior lobe has a wide influence in the body, being concerned particularly with growth in height, the development of the muscles, bones and reproductive system. It has also something to do with the handling of various foodstuffs. The middle and posterior lobes have to do with blood pressure, the handling of water and sugar and the excretion of urine. The whole gland in some way has to do with sleep. Deficiency of the pituitary in early years is associated with lack of stature, which may amount to dwarfism when it is severe, or merely to a less than average height when it is less severe. There may be lack of sexual development. It is thought that deficiency of the posterior lobe in such persons leads also to marked obesity. Tumors of the pituitary are associated many times with overactivity of this gland. If this occurs in early years the stature is apt to be more than normal and may amount to that of a giant. If it occurs in later years after growth has been completed, a condition known as acroniegaly results. The brows become beetling and overhanging, the soft tissues of the face are increased in amount, the lower jaw becomes undershot and the chin protrudes, and the hands and feet enlarge markedly. The THYROID is located in the neck, sitting astride the windpipe much like a saddle. It has been likened to the draft of a furnace or the ignition system of an automobile. No cell in the body reaches a stage of physiological completeness without an adequate amount of thyroid secretion. Goiter is enlargement of the thyroid. There are many varieties of goiter, which may not be associated with overactivity or hyperthyroidism. One variety known as exophthalmic goiter leads to a pop-
Proton motive force generation by citrolactic fermentation in Leuconostoc mesenteroides

In Leuconostoc mesenteroides subsp. mesenteroides 19D, citrate is transported by a secondary citrate carrier (CitP). Previous studies of the kinetics and mechanism of CitP performed in membrane vesicles of L. mesenteroides showed that CitP catalyzes divalent citrate HCit2-/H+ symport, indicative of metabolic energy generation by citrate metabolism via a secondary mechanism (C. Marty-Teysset, J. S. Lolkema, P. Schmitt, C. Divies, and W. N. Konings, J. Biol. Chem. 270:25370-25376, 1995). This study also revealed an efficient exchange of citrate and D-lactate, a product of citrate/carbohydrate cometabolism, suggesting that under physiological conditions, CitP may function as a precursor/product exchanger rather than a symporter. In this paper, the energetic consequences of citrate metabolism were investigated in resting cells of L. mesenteroides. The generation of metabolic energy in the form of a pH gradient (delta pH) and a membrane potential (delta psi) by citrate metabolism was found to be largely dependent on cometabolism with glucose. Furthermore, in the presence of glucose, the rates of citrate utilization and of pyruvate and lactate production were strongly increased, indicating an enhancement of citrate metabolism by glucose metabolism. The rate of citrate metabolism under these conditions was slowed down by the presence of a membrane potential across the cytoplasmic membrane. The production of D-lactate inside the cell during cometabolism was shown to be responsible for the enhancement of the electrogenic uptake of citrate. Cells loaded with D-lactate generated a delta psi upon dilution in buffer containing citrate, and cells incubated with citrate built up a pH gradient upon addition of D-lactate. The results are consistent with an electrogenic citrate/D-lactate exchange generating in vivo metabolic energy in the form of a proton electrochemical gradient across the membrane. The generation of metabolic energy from citrate metabolism in L. mesenteroides may contribute significantly to the growth advantage observed during cometabolism of citrate and glucose.
The fourth dimension in immunological space: how the struggle for nutrients selects high‐affinity lymphocytes

Lymphocyte activation via the antigen receptor is associated with radical shifts in metabolism and changes in requirements for nutrients and cytokines. Concomitantly, drastic changes occur in the expression of pro‐and anti‐apoptotic proteins that alter the sensitivity of lymphocytes to limiting concentrations of key survival factors. Antigen affinity is a primary determinant for the capacity of activated lymphocytes to access these vital resources. The shift in metabolic needs and the variable access to key survival factors is used by the immune system to eliminate activated low‐affinity cells and to generate an optimal high‐affinity response. In this review, we focus on the control of apoptosis regulators in activated lymphocytes by nutrients, cytokines, and costimulation. We propose that the struggle among individual clones that leads to the formation of high‐affinity effector cell populations is in effect an ‘invisible’ fourth signal required for effective immune responses.
Draft Genome Sequences of Four Vibrio parahaemolyticus Isolates from Clinical Cases in Canada

ABSTRACT Vibrio parahaemolyticus is a leading cause of bacterial gastroenteritis following ingestion of contaminated seafood. This report presents the draft genome sequences of four clinical strains of V. parahaemolyticus isolated in Canada. All four strains lack traditional pathogenic markers and possess uniquely individual characteristics identified using other typing criteria.
Fast hybrid algorithms for PET image reconstruction

We describe a hybrid approach to iterative PET image reconstruction in which we combine three algorithms: preconditioned conjugate gradient (PCG), ordered subsets separable paraboloidal surrogate (OSSPS), and emission reconstruction incremental optimization transfer (ERIOT). These algorithms exhibit quite different convergence behavior, e.g. the initial convergence of OSSPS is fast but it soon enters a limit cycle. Conversely, initial convergence of PCG is slow compared to OSSPS and ERIOT but its asymptotic behavior is the fastest. The hybrid approach estimates convergence behavior for each method by fitting an exponential to the objective function as a function of iteration number and switches between the algorithms to optimize the convergence behavior throughout the iterations. This hybrid approach is compared to each of the component algorithms in application to simulated PET data demonstrating a reduction of at least 50% in iterations required for effective convergence compared to use of PCG alone.
Variation in the qualities of instruction methods adopted by different Kindergartens in Hong Kong

This study examined the learning and teaching approaches used in three kindergartens in Hong Kong. The kindergartens used the same curriculum package and were assessed as being of “good”, “acceptable” and “unsatisfactory” quality, respectively, by the regulatory body. The participants were five kindergarten teachers and their students, and five specialists in pre-primary education who provided an independent assessment of kindergarten quality. Each teacher was observed for three hours a day over three consecutive days. The specialists discussed videotaped observations of learning activities from each of the kindergartens in a focus group, and rated kindergarten quality. The results indicated that the ratings of the regulatory body and the specialists were consistent and appeared to be informed by the criteria for “developmentally appropriate practices”. The low-quality classroom was teacher-directed, engaged mainly in chalk-and talk and paper-and-pencil activities, and involved few interactions between the teacher and the children or among the children. The children in the other two kindergartens engaged in authentic learning activities, learned in small groups, appeared cognitively engaged and had many interactions with the teacher and other children. Although the kindergartens claimed to use the Montessori, Project and Unit approaches, the specialists felt that none of them actually implemented their purported approaches with fidelity. On the basis of these findings, suggestions are made to improve the quality of learning and teaching in pre-primary schools.
Thalamic-Evoked Synaptic Interactions in Barrel Cortex Revealed by Optical Imaging

We used optical imaging of voltage-sensitive dye signals to study the spatiotemporal spread of activity in the mouse barrel cortex, evoked by stimulation of thalamocortical afferents in an in vitro slice preparation. Stimulation of the thalamus, at low current intensity, results in activity largely restricted to a single barrel, and to the border between layers Vb and VI. Low concentrations of the GABAA receptor antagonist bicuculline increase the amplitude of the optical signals, without affecting their spatiotemporal propagation. Higher concentrations of bicuculline result in paroxysmal activity, which propagates via intracolumnar and intercolumnar excitatory pathways. Enhancing the activity of NMDA receptors, by removing Mg2+ from the extracellular solution, dramatically alters the spatiotemporal pattern of excitation: activity spreads to supragranular and infragranular layers and adjacent barrel columns. This enhanced propagation is suppressed by the NMDA receptor antagonist AP5. A similar enhancement of activity propagation can be produced by stimulating the thalamus with a short, high-frequency pulse train. Application of AP5 suppresses the frequency-dependent spread of activity. These findings indicate that the spatiotemporal spread of activity in the barrel cortex is altered by varying the temporal patterns of thalamic inputs, via an NMDA receptor-mediated mechanism, and suggest that a similar process occurs during repetitive whisking activity.
Gene Expression in B-1 Cells from Lupus-Prone Mice

New Zealand Black X New Zealand White F1 [(NZB/NZW)F1] mice develop an autoimmune condition with similarities to human systemic lupus erythematosus (SLE). In this study, we demonstrate that B-1 cells, which have previously been reported to be involved in several autoimmune diseases, have altered gene expression in these mice. RNA was extracted from purified B-1 cells of disease-free C57BL/6 mice and lupus-prone (NZB/NZW)F1 mice. Gene expression was analysed using DNA microarray techniques and validated by real time reverse transcriptase polymerase chain reaction (RT-PCR). In (NZB/NZW)F1 mice, some genes had altered expression patterns compared to disease-free controls. Specifically, the upregulation of Ifitm1, Pvrl2 and Ifi202b and downregulation of Trp53bp1 mRNA were observed in (NZB/NZW)F1 mice. These genes are known to be associated with autoimmune diseases. This pattern of gene expression in B-1 cells could understanding of the pathogenesis of SLE. Thus, it is reasonable to hypothesise that the altered gene expression observed in B-1 cells in our experimental model is important for SLE prognosis and therapy, and these implications are discussed herein.
Control flow driven splitting of loop nests at the source code level

This paper presents a novel source code transformation for control flow optimization called loop nest splitting which minimizes the number of executed if-statements in loop nests of embedded multimedia applications. The goal of the optimization is to reduce runtimes and energy consumption. The analysis techniques are based on precise mathematical models combined with genetic algorithms. Due to the inherent portability of source code transformations, a very detailed benchmarking using 10 different processors can be performed. The application of our implemented algorithms to three real-life multimedia benchmarks leads to average speed-ups by 23.6%-62.1% and energy savings by 19.6%-57.7%. Furthermore, our optimization also leads to advantageous pipeline and cache performance.
Expression of klotho and β-catenin in esophageal squamous cell carcinoma, and their clinicopathological and prognostic significance.

Esophageal carcinoma is one of the most common types of cancers in the world; the molecular mechanism underlying its tumorigenesis is still not well understood. This study was aimed at investigating the expression of klotho and β-catenin in patients with esophageal squamous cell carcinoma (ESCC) and analyzing their association with clinicopathological variables and their effects on prognosis. The expression patterns of klotho and β-catenin were determined by tissue microarray and immunohistochemical technique in ESCC and normal tissues, and their correlations with clinicopathological characteristics were investigated using univariate and multivariate analysis. The serum klotho levels in 40 ESCC patients and controls were measured by sandwich enzyme-linked immunosorbent assay system (ELISA). The expression level of klotho was significantly lower in ESCC than in the adjacent noncancerous tissues (30 vs. 50%, P < 0.000), and the protein level was negative correlated with clinical staging, histological grade, lymph node metastasis, and invasion depth (P < 0.05). Whereas, the expression of β-catenin was much higher in ESCC than their corresponding normal mucosa tissues (78.3 vs. 11.5%, P < 0.000), and the level of protein correlated only with histological grade and invasion depth (P < 0.05). Correlation analysis showed the expression level of klotho inversely correlated with that of β-catenin (r = -0.214, P < 0.01). Patients with klotho-positive tumors had longer survival than those with klotho-negative tumors (P < 0.01). Cox proportional hazards model analysis demonstrated that positive expression of klotho was an important factor indicating good prognosis (hazard ratio, 0.371; 95% confidence interval, 0.201-0.685; P < 0.01). ELISA showed that the level of serum klotho was markedly higher (461.50 ± 43.30 pg/mL) than control group (239.37 ± 20.65 pg/mL) (P < 0.001). Receiver operating characteristic analysis gave a cut-off value of 327.031 of serum klotho with a sensitivity of 81.3% and specificity of 81.2% (P < 0.000). Our present study demonstrated for the first time that klotho might be a novel biomarker candidate for predicting progression and prognosis in patients with ESCC.
Human vascular adhesion protein 1 (VAP-1) is a unique sialoglycoprotein that mediates carbohydrate-dependent binding of lymphocytes to endothelial cells

The regulated interactions of leukocytes with vascular endothelial cells are crucial in controlling leukocyte traffic between blood and tissues. Vascular adhesion protein-1 (VAP-1) is a novel, human endothelial cell molecule that mediates tissue-selective lymphocyte binding. Two species (90 and 170 kD) of VAP-1 exist in lymphoid tissues. Glycosidase digestions revealed that the mature 170-kD form of VAP-1 expressed on the lumenal surfaces of vessels is a heavily sialylated glycoprotein. The sialic acids are indispensable for the function of VAP-1, since the desialylated form of VAP-1 no longer mediates lymphocyte binding. We also show that L-selectin is not required for binding of activated lymphocytes to VAP-1 under conditions of shear stress. The 90-kD form of VAP-1 was only seen in an organ culture model, and may represent a monomeric or proteolytic form of the larger species. These data indicate that L-selectin negative lymphocytes can bind to tonsillar venules via the VAP- 1-mediated pathway. Moreover, our findings extend the role of carbohydrate- mediated binding in lymphocyte-endothelial cell interactions beyond the known selectins. In conclusion, VAP-1 naturally exists as a 170-kD sialoglycoprotein that uses sialic acid residues to interact with its counter-receptors on lymphocytes under nonstatic conditions.
Reconstitution of TGFBR2-Mediated Signaling Causes Upregulation of GDF-15 in HCT116 Colorectal Cancer Cells

Although inactivating frameshift mutations in the Transforming growth factor beta receptor type 2 (TGFBR2) gene are considered as drivers of microsatellite unstable (MSI) colorectal tumorigenesis, consequential alterations of the downstream target proteome are not resolved completely. Applying a click-it chemistry protein labeling approach combined with mass spectrometry in a MSI colorectal cancer model cell line, we identified 21 de novo synthesized proteins differentially expressed upon reconstituted TGFBR2 expression. One candidate gene, the TGF-ß family member Growth differentiation factor-15 (GDF-15), exhibited TGFBR2-dependent transcriptional upregulation causing increased intracellular and extracellular protein levels. As a new TGFBR2 target gene it may provide a link between the TGF-ß branch and the BMP/GDF branch of SMAD-mediated signaling.
Laser beam measurement of abdominal sagittal diameter in obese children: a validation study

What is already known about this subject Sagittal diameter (SAD), i.e. the mid height of the abdomen when lying down, has been reported to correlate to visceral fat, insulin resistance and cardiovascular risk factors in adults. SAD seems to be the best anthropometric predictor of cardiovascular risk, and also of more importance than waist circumference (WC) in adults. There has been no validation studies comparing SAD measured with anthropometric tools (e.g. ruler) to measurements made with more exact devices such as magnetic resonance imaging (MRI) in pediatric age.