Miracle-dz/UniFAR-FTUs huggingface dataset:
Intestinal absorption and permeability in paediatric short-bowel syndrome: a pilot study.

BACKGROUND Sugar absorption tests are an effective, noninvasive way to assess intestinal permeability. The role of intestinal barrier integrity in complications and outcome of short-bowel syndrome is not known. The purpose of the study was to evaluate whether such tests provide information on the status of intestinal mucosa of these patients. METHODS Six children with short-bowel syndrome--median age, 12 months, and median small bowel length at birth, 30 cm--had a sugar test with 3-o-methyl-D-glucose, D-xylose, D-rhamnose, and melibiose approximately 2 months after operation. The melibiose/L-rhamnose ratio was used as an index of permeability, and percentages of 3-o-methyl-D-glucose and D-xylose absorbed were used as indices of absorption. Parenteral nutrition requirement, bowel length, liver disease, recent sepsis, and bacterial overgrowth were recorded. RESULTS Three patients had increased permeability, and all of them had had a recent episode of sepsis and severe liver disease. All subjects had malabsorption of 3-o-methyl-D-glucose, and five of six had malabsorption of D-xylose and L-rhamnose. The absorption of 3-o-methyl-D-glucose correlated with bowel length (r2 = 0.78; P = 0.04), whereas the absorption of D-xylose correlated with parenteral requirement (r2 = 0.66; P = 0.04) at that time. CONCLUSIONS Increased permeability was observed in three of six patients with short-bowel syndrome associated with a recent episode of sepsis and severe liver disease. Other indices of malabsorption correlated significantly with different clinical features of the disease. A prospective larger scale study in a homogeneous population is indicated to assess at multiple points during the disease course whether the test can be helpful in the management of these patients.
Substrate Affinity Differentially Influences Protein Kinase C Regulation and Inhibitor Potency*

The overlapping network of kinase-substrate interactions provides exquisite specificity in cell signaling pathways, but also presents challenges to our ability to understand the mechanistic basis of biological processes. Efforts to dissect kinase-substrate interactions have been particularly limited by their inherently transient nature. Here, we use a library of FRET sensors to monitor these transient complexes, specifically examining weak interactions between the catalytic domain of protein kinase Cα and 14 substrate peptides. Combining results from this assay platform with those from standard kinase activity assays yields four novel insights into the kinase-substrate interaction. First, preferential binding of non-phosphorylated versus phosphorylated substrates leads to enhanced kinase-specific activity. Second, kinase-specific activity is inversely correlated with substrate binding affinity. Third, high affinity substrates can suppress phosphorylation of their low affinity counterparts. Finally, the substrate-competitive inhibitor bisindolylmaleimide I displaces low affinity substrates more potently leading to substrate selective inhibition of kinase activity. Overall, our approach complements existing structural and biophysical approaches to provide generalizable insights into the regulation of kinase activity.
Do Single Nucleotide Polymorphisms in Xenobiotic Metabolizing Genes Determine Breast Cancer Susceptibility and Treatment Outcomes?

SNPs in CYP1A1, CYP2A1, CYP2B6, CYP2C, CYP2D6, CYP3A, GSTM1, GSTT1, GSTP1, SULT1A1, SULT1A2, UGT, and MTHFR are associated with breast cancer susceptibility; however, lack of such associations are also reported in some populations. The contradictory findings are explained on the basis of ethnic variation among populations and due to lack of proper sample size, detailed genotype-phenotype combinations and validation of gene expression studies at protein level. In this review, SNPs in these genes that have tremendous potential in identification of susceptible individuals, development of preventive strategies, treatment outcomes and their limitations are discussed.
Description of Perkinsus andrewsi n. sp. Isolated from the Baltic Clam (Macoma balthica) by Characterization of the Ribosomal RNA Locus, and Development of a Species-Specific PCR-Based Diagnostic Assay

Abstract A Perkinsus species was isolated from the baltic clam Macoma balthica and an in vitro culture established under conditions described for P. marinus. As reported previously, morphological features remarkable enough to clearly indicate that this isolate is a distinct Perkinsus species were lacking. In this study, regions of the rRNA locus (NTS, 18S, ITS1, 5.8S, and ITS2) of this isolate were cloned, sequenced, and compared by alignment with those available for other Perkinsus species and isolates. Sequence data from the rRNA locus and species-specific PCR assays indicated not only that Perkinsus sp. from M. balthica was not P. marinus, but it was different from P. atlanticus and P. olseni. The degree of difference was comparable to or greater than differences between accepted Perkinsus species. In particular, NTS sequence and length were dramatically different from that of P. marinus and P. atlanticus. Therefore, we formally propose to designate the Perkinsus sp. from M. balthica as a separate species, P. andrewsi n. sp. Primers based on P. andrewsi NTS sequence were used to develop a PCR-based diagnostic assay that was validated for species-specificity and sensitivity. PCR-based assays specific for either P. andrewsi or P. marinus were used to test for their presence in bivalve species sympatric to M. balthica. Although isolated from M. balthica, P. andrewsi was also detected in the oyster Crassostrea virginica and clams Macoma mitchelli and Mercenaria mercenaria, and could coexist with P. marinus in all four bivalve species tested.
Molecular cloning of the region of the terminus of Escherichia coli K-12 DNA replication

A series of plasmids have been isolated either by ligation of defined restriction fragments to plasmid pBR325 or by screening of a cosmid bank by in situ colony hybridization. Together with one previously isolated plasmid, they spanned 86% of the 30.5- to 34-min region of the genetic map of Escherichia coli K-12. Physical analysis of these plasmids and hybridizations to Southern blots confirmed the endonuclease map of this region, with the exception of a 9.3-kilobase pair inversion.
Cloning, Expression and Hormonal Regulation of Steroidogenic Acute Regulatory Protein Gene in Buffalo Ovary

In mammalian ovary, steroidogenic acute regulatory (StAR) protein mediates the true rate-limiting step of transport of cholesterol from outer to inner mitochondrial membrane. Appropriate expression of StAR gene represents an indispensable component of steroidogenesis and its regulation has been found to be species specific. However, limited information is available regarding StAR gene expression during estrous cycle in buffalo ovary. In the present study, expression, localization and hormonal regulation of StAR mRNA were analyzed by semi-quantitative RT-PCR in buffalo ovary and partial cDNA was cloned. Total RNA was isolated from whole follicles of different sizes, granulosa cells from different size follicles and postovulatory structures like corpus luteum and Corpus albicans. Semi-quantitative RT-PCR analyses showed StAR mRNA expression in the postovulatory structure, corpus luteum. No StAR mRNA was detected in total RNA isolated from whole follicles of different size including the preovulatory follicle (>9 mm in diameter). However, granulosa cells isolated from preovulatory follicles showed the moderate expression of StAR mRNA. To assess the hormonal regulation of StAR mRNA, primary culture of buffalo granulosa cells were treated with FSH (100 ng/ml) alone or along with IGF-I (100 ng/ml) for 12 to 18 h. The abundance of StAR mRNA increased in cells treated with FSH alone or FSH with IGF-I. However, effect of FSH with IGF-I on mRNA expression was found highly significant (p<0.01). In conclusion, differential expression of StAR messages was observed during estrous cycle in buffalo ovary. Also, there was a synergistic action of IGF-I on FSH stimulation of StAR gene.
Refreshing Refreshable Braille Displays

The increased access to books afforded to blind people via e-publishing has given them long-sought independence for both recreational and educational reading. In most cases, blind readers access materials using speech output. For some content such as highly technical texts, music, and graphics, speech is not an appropriate access modality as it does not promote deep understanding. Therefore blind braille readers often prefer electronic braille displays. But, these are prohibitively expensive. The search is on, therefore, for a low-cost refreshable display that would go beyond current technologies and deliver graphical content as well as text. And many solutions have been proposed, some of which reduce costs by restricting the number of characters that can be displayed, even down to a single braille cell. In this paper, we demonstrate that restricting tactile cues during braille reading leads to poorer performance in a letter recognition task. In particular, we show that lack of sliding contact between the fingertip and the braille reading surface results in more errors and that the number of errors increases as a function of presentation speed. These findings suggest that single cell displays which do not incorporate sliding contact are likely to be less effective for braille reading.
Avian Pox in Sanderlings from Florida

Avian pox was diagnosed in three sanderlings (Calidris alba) on Sanibel Island, Florida (USA) in February 1997. All three cases had large tumor-like lesions which contributed significantly to their mortality. Poxvirus infection was confirmed by cytology, histopathology, and electron microscopy. This is the first report of poxvirus infection in sanderlings.
A retrospective review of blood transfusions in cancer patients with anemia.

BACKGROUND The factors contributing to blood transfusions in patients with anemia of chronic disease are not well documented in the literature. We analyzed all blood transfusion events within a single oncology practice to determine if certain chemotherapy drugs, cancer types, or other factors necessitated more frequent transfusions. PATIENTS AND METHODS Out of 331 patients receiving chemotherapy, 103 (31%) patients received a blood transfusion in 1995. Each of these charts was reviewed and sorted by diagnosis, treatment medications, and past transfusion and/or treatment history. Hemoglobin levels were obtained for each transfusion received in 1995. RESULTS The average hemoglobin at time of transfusion was 7.9 g/dl. Higher hemoglobin levels at transfusion were observed for patients over the age of 60 and patients who received prior chemotherapy. Lower hemoglobin levels at transfusion were observed for patients receiving Epoetin Alfa and sarcoma patients. The average number of red blood cell (RBC) units transfused in 1995 was 5.1 per patient. More units were given to patients receiving etoposide, while fewer units were given to those receiving ifosfamide. We created a transfusion severity index (TSI) to jointly measure these two variables. CONCLUSION The results of this study identify transfusion needs associated with certain groups of cancer patients and with certain types of chemotherapy drugs.
Efficiency assessment of effluent treatment plant (ETP) treating an automobile industry effluent (Sidcul) Haridwar.

Water is an integral part of life on this planet but nowadays this precious thing is continuously getting polluted due to different activities. Industrial sector is one and most polluting agent among all of them. The effluents generated from the automobile industries, creates an environmental hazard near the disposal site and in its vicinity. Workers are exposed to occupational and other health hazards when they are exposed to the air and drinking water, which may get polluted due to spraying of the paints. Mostly alkyd paint is used for painting process. A large amount of water is used and polluted during such industrial processes. Wastewater of the automobile industries not only contains high levels of suspended and total solids such as oil and grease and colouring, at various stages of manufacturing but also, a significant amount of dissolved organics, resulting in high BOD or COD loads. The study reveals the performance evaluation of effluent treatment plant and its treatability. During the present study the samples were collected from each site at an interval of 10 days from an automobile industry located in IIE, SIDCUL Haridwar. The collected samples were analysed for Temperature, Total solid, Total dissolved solids, Total suspended solids, pH, Dissolved oxygen, Biological oxygen demand, Chemical oxygen demand and oil & grease. During the present study oil & grease in untreated effluent ranged from 19mg/l to 28mg/l and in treated effluent from 1.9mg/l to 4.1mg/l. Chemical oxygen demand in untreated effluent ranged from 2300mg/l to 2700mg/l and in treated effluent from 38mg/l to 57mg/l. pH in untreated effluent ranged from 7.1 to 8.3 and in treated effluent from 6.7 to 8.3. The results revealed that the performance of effluent treatment plant of automobile industry is satisfactory.
Application of quantitative analysis to biologic profile evaluation in breast cancer

Background. The biologic profile of 907 infiltrating breast carcinomas was determined considering estrogen receptor (ER) and progesterone receptor (PR), proliferation index (PI) and c‐erbB‐2/Neu expression. The relationship with pathologic parameters (lymph node status, size, histotype) were studied by a multivariate analysis. The clinical prognostic power of biologic profile also was evaluated for 265 patients.
f¨ur Mathematik in den Naturwissenschaften Leipzig Hierarchical Singular Value Decomposition of Tensors

We deﬁne the hierarchical singular value decomposition (SVD) for tensors of order d ≥ 2. This hierarchical SVD has properties like the matrix SVD (and collapses to the SVD in d = 2), and we prove these. In particular, one can ﬁnd low rank (almost) best approximations in a hierarchical format ( H -Tucker) which requires only O (( d − 1) k 3 + dnk ) data, where d is the order of the tensor, n the size of the modes and k the rank. The H -Tucker format is a specialization of the Tucker format and it contains as a special case all (canonical) rank k tensors. Based on this new concept of a hierarchical SVD we present algorithms for hierarchical tensor calculations allowing for a rigorous error analysis. The complexity of the truncation (ﬁnding lower rank approximations to hierarchical rank k tensors) is in O (( d − 1) k 4 + dnk 2 ) and the attainable accuracy is just 2–3 digits less than machine precision.
Cardiac release of cytokines and inflammatory responses in acute myocardial infarction.

BACKGROUND In animal models of myocardial infarction (MI), inflammatory responses compromise microcirculation during reperfusion and restrict functional recovery. To investigate cardiac inflammatory responses in patients with acute MI, we examined the cardiac release of cytokines, the expression on neutrophils of the beta 2-integrin Mac-1 (CD11b/CD18) and L-selectin (CD62L), and the cardiac release of thrombomodulin as a marker of endothelial injury. METHODS AND RESULTS In 12 patients with acute anterior MI, blood samples were obtained from the coronary sinus and from the aorta immediately before and after recanalization of the coronary occlusion by balloon angioplasty. Twelve patients undergoing elective balloon angioplasty served as control subjects. Plasma concentrations of interleukin (IL)-1 beta, IL-6, IL-8, tumor necrosis factor-alpha, and thrombomodulin were determined by immunoassay, and surface expression of CD11b and CD62L was assessed by flow cytometry. Differences in coronary sinus and arterial blood were found in IL-6 before (median, 6.3 ng/L, P = .01) and after (13.4 ng/L, P = .002) recanalization and in IL-8 after recanalization (10.7 ng/L, P = .02). The cardiac release of both cytokines significantly (P < or = .03) increased with reperfusion. Cytokine release after reperfusion was associated with significant transcardiac gradients in surface expression on neutrophils of CD11b (10.1 mean channel of fluorescence intensity [mean fl], P = .01) and CD62L (-87 mean fl, P = .007) and with a thrombomodulin release (4.5 micrograms/L, P = .004). Transcardiac gradients in IL-1 beta and tumor necrosis factor-alpha were not found. None of the changes found in MI were detectable in the control group. CONCLUSIONS As evidence of cardiac inflammatory responses in reperfused acute MI, the study demonstrates cardiac neutrophil activation with signs of endothelial injury and a release of the proinflammatory cytokines IL-8 and IL-6. These findings may assist in the design of pharmacological interventions aimed at reducing microvascular reperfusion injury.
Cancer metastasis facilitated by developmental pathways: Sonic hedgehog, Notch, and bone morphogenic proteins

This review will highlight the significance of three critical pathways in developmental biology and our emerging understanding of their roles in regulating tumor metastasis: Bone morphogenic protein (BMP), Notch and Sonic hedgehog (SHH). We will discuss parallels between their known roles in development and how these processes can be used by tumor cells to create microenvironments that enhance tumor metastasis. That tumor cells usurp pathways critical to the developing embryo is not surprising, as many of the normal developmental programs include processes that are also seen during tumor progression to a metastatic phenotype, including epithelial to mesenchymal transition (EMT), tissue specific morphogenesis, cellular motility and invasion. BMPs are involved in EMT, contribute to tissue specific morphogenesis, and are expressed in highly‐metastatic tumor cells. BMPs have also been hypothesized to have a role in the establishment of a pre‐neoplastic niche. Notch and SHH facilitate neovascularization, angiogenesis, EMT and can contribute to the maintenance of highly‐metastatic tumor stem cells. J. Cell. Biochem. 102: 829–839, 2007. © 2007 Wiley‐Liss, Inc.
Intuitive muscle-gesture based robot navigation control using wearable gesture armband

In this paper, we propose a muscle gesture-computer interface (MGCI) system for robot navigation control employing a commercial wearable MYO gesture control armband, the motion and gesture control device from Thalmic Labs. This system allows the user to control a three-wheeled omni-directional robot remotely by his/her intuitive motion. Two approaches were proposed with surface electromyographic (sEMG) sensors and combination of sEMG and inertial measurement unit (EMU). Computer simulations and experiments were conducted to evaluate the feasibility of the proposed system.
Facial morphology as an indicator of genetic predisposition to cleft lip and palate.

It is clear that heredity plays a major role in the genesis of cleft lip and palate, although the mode of inheritance remains unresolved [1-5]. Falconer [6] and Carter [7] have proposed a multifactorial threshold model for inheritance of some congenital diseases including clefts of the lip and palate. Recently this model has received support from several authors, particularly for cleft lip with or without cleft palate [8-11]. Trasler [12] suggested that variation in susceptibility to cleft lip among certain strains of mice might be related to variation in embryonic face shape. A pilot study by Fraser and Pashayan [13] using soft tissue measurements and physioprints indicated that the parents of children with cleft lip with or without cleft palate tended to have a longer interocular-to-chin dimension, wider dizygomatic diameter, underdeveloped maxillae, fewer ovoid face shapes, and more thin upper lips than the control group. Coccaro et al. [14], using measurements from lateral cephalometric radiographs, concluded that parents of children with cleft lip with or without cleft palate have less convex faces with a tendency toward mandibular prognathism and have shorter vertical and horizontal measurements of the upper face than the control group. Niswander et al. [15], using a smaller sample from the population reported here, showed increased interorbital distance in parents of cleft children. Collectively, these studies suggest that the parents of children with cleft lip and palate might have some morphological features different from the rest of the population. However, some differences exist in the findings of the studies reported to date. Although they did not directly measure it, Fraser and Pashayan's [13] study did not support the finding of a shorter upper facial height in the experimental group as revealed in the study of Coccaro et al. [14]; rather, they found longer interocular-chin measurements, suggesting the converse. Also the former study did not show the increased interorbital distance as indicated by Niswander et al. [ 15]. Using a larger sample and controlling for sex and dental status, we attempt here (1) to reexamine whether there are significant features of facial morphology
A methodology for constructing maintainability model of object-oriented design

It is obvious that qualities of software design heavily affects on qualities of software ultimately developed. One of claimed advantages of object-oriented paradigm is the ease of maintenance. The main goal of this work is to propose a methodology for constructing maintainability model of object-oriented software design model using three techniques. Two subcharacteristics of maintainability: understandability and modifiability are focused in this work. A controlled experiment is performed in order to construct maintainability models of object-oriented designs using the experimental data. The first maintainability model is constructed using metrics-discriminant technique. This technique analyzes the pattern of correlation between maintainability levels and structural complexity design metrics applying discriminant analysis. The second one is built using weighted-score-level technique. The technique uses a weighted sum method by combining understandability and modifiability levels which are converted from understandability and modifiability scores. The third one is created using weighted-predicted-level technique. Weighted-predicted-level uses a weighted sum method by combining predicted understandability and modifiability level, obtained from applying understandability and modifiability models. This work presents comparison of maintainability models obtained from three techniques.