gebhart/patrepeval huggingface dataset:
Advances in Surgical Treatment of Male Infertility (2012)

A male factor is the only cause of infertility in 30% to 40% of couples. Most causes of male infertility are treatable, and the goal of many treatments is to restore the ability to conceive naturally. Varicoceles are present in 15% of the normal male population and in approximately 40% of men with infertility. Varicocele is the most common cause of male infertility that can be corrected surgically. In males with azoospermia, the most common cause is post-vasectomy status. Approximately 6% of males who undergo vasectomy eventually seek reversal surgery. Success of vasectomy reversal decreases with the number of years between vasectomy and vasovasostomy. Other causes of obstructive azoospermia include epididymal, vasal or ejaculatory duct abnormalities. Epididymal obstruction is the most common cause of obstructive azoospermia. Patients with epididymal obstruction without other anatomical abnormalities can be considered as candidates for vasoepididymostomy. With microsurgical techniques, success of patency restoration can reach 70~90%. In case of surgically uncorrectable obstructive azoospermia, sperm extraction or aspiration for in vitro fertilization is needed. Nonobstructive azoospermia is the most challenging type of male infertility. However, microsurgical testicular sperm extraction may be an effective method for nonobstructive azoospermia patients.
Correction: Computational Modeling Reveals Distinct Effects of HIV and History of Drug Use on Decision-Making Processes in Women (2013)

Objective: Drug users and HIV-seropositive individuals often show deficits in decision-making; however the nature of these deficits is not well understood. Recent studies have employed computational modeling approaches to disentangle the psychological processes involved in decision-making. Although such approaches have been used successfully with a number of clinical groups including drug users, no study to date has used computational modeling to examine the effects of HIV on decision-making. In this study, we use this approach to investigate the effects of HIV and drug use on decisionmaking processes in women, who remain a relatively understudied population.
Synthesis of Glass‐like Cordierite from Metal Alkoxides and Characterization by <sup>27</sup> Al and <sup>29</sup> Si MASNMR (1990)

A sol‐gel process for the preparation of glass‐like cordierite and ceramic oxide powder is described. Metal alkoxide precursors were dissolved in 2‐methoxyethanol and the metal cations were complexed using 2,4‐pentanedione to overcome different hydrolysis rates of metal alkoxides which lead to microscopic inhomogeneities during gelation. Heating the gel in an aerated furnace resulted in ultrafine cordierite powder of stoichiometric composition at a relatively low temperature. Cordierite gel and glass were also prepared by other methods and compared with the above gel. The environments of aluminum and silicon in the glass and gels heated at various temperatures were studied using 27 Al and 29 Si magic angle spinning nuclear magnetic resonance (MASNMR) spectroscopy. Most of the heated gels and the glass showed resonances due to pentacoordinated aluminum along with 4‐ and 6‐coordinated aluminum. The homogeneities of the resulting gels and glass are compared using the MASNMR data.
A Semiautomated Procedure for Total Nitrogen in Plant and Soil Samples (1976)

Abstract This study evaluated inexpensive alternatives for the determination of total N in plant and soil samples. Plant and soil samples which varied widely in N concentration were digested in a 126‐sample‐capacity Al block digester followed by determination of total N with the ammonium electrode in a semiautomated reaction vessel assembly. The proposed Ammonium electrode semiautomated (AES) procedure was compared to standard micro‐Kjeldahl and aluminum block digested‐steam distilled‐titrated (ABDDT) procedures. Thirty to 50 more samples could be analyzed per 8‐hour day with the proposed semiautomated procedure as compared to standard micro‐Kjeldahl methods. The precision of the methods were comparable but significantly more N was found by using the ABDDT procedure.
C‐Terminal‐Sequence Determination by Carboxypeptidase C from Orange Leaves (1972)

Carboxypeptidase C isolated from orange leaves has been investigated for its use in C‐terminal sequence determinations. The sequence of the first six C‐terminal residues of the denatured protein ribonuclease could be deduced unequivocally from a time‐release plot of an incubation mixture containing 1 mole % of the enzyme. No release of free amino acids by autodigestion of the enzyme could be detected after prolonged periods of incubation. Three different peptides have been degraded demonstrating sufficient and comparable rates of release of all protein amino acids, including proline. Thus the enzyme reveals a broad specificity for acidic, neutral and basic amino acids and combines the activity and specificity of the pancreatic carboxypeptidases A and B, but in addition releases the imino acid proline.
Role of Cl− in Electrogenic Na+-coupled Cotransporters GAT1 and SGLT1 (2000)

We have investigated the functional role of Cl(-) in the human Na(+)/Cl(-)/gamma-aminobutyric acid (GABA) and Na(+)/glucose cotransporters (GAT1 and SGLT1, respectively) expressed in Xenopus laevis oocytes. Substrate-evoked steady-state inward currents were examined in the presence and absence of external Cl(-). Replacement of Cl(-) by gluconate or 2-(N-morpholino)ethanesulfonic acid decreased the apparent affinity of GAT1 and SGLT1 for Na(+) and the organic substrate. In the absence of substrate, GAT1 and SGLT1 exhibited charge movements that manifested as pre-steady-state current transients. Removal of Cl(-) shifted the voltage dependence of charge movements to more negative potentials, with apparent affinity constants (K(0.5)) for Cl(-) of 21 and 115 mm for SGLT1 and GAT1, respectively. The maximum charge moved and the apparent valence were not altered. GAT1 stoichiometry was determined by measuring GABA-evoked currents and the unidirectional influx of (36)Cl(-), (22)Na(+), or [(3)H]GABA. Uptake of each GABA molecule was accompanied by inward movement of 2 positive charges, which was entirely accounted for by the influx of Na(+) in the presence or absence of Cl(-). Thus, the GAT1 stoichiometry was 2Na(+):1GABA. However, Cl(-) was transported by GAT1 because the inward movement of 2 positive charges was accompanied by the influx of one Cl(-) ion, suggesting unidirectional influx of 2Na(+):1Cl(-):1GABA per transport cycle. Activation of forward Na(+)/Cl(-)/GABA transport evoked (36)Cl(-) efflux and was blocked by the inhibitor SKF 89976A. These data suggest a Cl(-)/Cl(-) exchange mechanism during the GAT1 transport cycle. In contrast, Cl(-) was not transported by SGLT1. Thus, in both GAT1 and SGLT1, Cl(-) modulates the kinetics of cotransport by altering Na(+) affinity, but does not contribute to net charge transported per transport cycle. We conclude that Cl(-) dependence per se is not a useful criterion to classify Na(+) cotransporters.
Real-time <i>in situ</i> detection and quantification of bacteria in the Arctic environment (2013)

At present, there are no methods that determine the total microbial load on an abiotic substrate in real time. The utility of such a capability ranges from sterilization and medical diagnostics to the search for new microorganisms in the environment and study of their ecological niches. We report the development of a hand-held, fluorescence detection device and demonstrate its applicability to the field detection of Arctic bacteria. This technology is based on the early pioneering work of Britton Chance which elucidated the intrinsic fluorescence of a number of metabolites and protein cofactors in cells, including reduced pyridine nucleotides, cytochromes and flavins. A PDA controls the device (fluorescence excitation and data collection) and processes the multiwavelength signals to yield bacterial cell counts, including estimates of live cells, dead cells and endospores. Unlike existing methods for cell counting, this method requires no sample contact or addition of reagents. The use of this technology is demonstrated with in situ measurements of two sub-glacial microbial communities at sites in Palander and colonized surface rocks in the Bockfjord Volcanic Complex during AMASE 2008 (Arctic Mars Analog Svalbard Expedition). The total bacterial load on the interrogated sample surfaces ranged from < 20 cells/cm 2 to > 10 9 cells/cm 2 .
Extracellular matrix remodeling at the early stages of liver regeneration in the rat (1997)

Previous studies have shown that activity of urokinase-type plasminogen activator (u-PA) increases very rapidly (within 1 minute) after partial hepatectomy. In view of the well-recognized roles of u-PA as one of the major initiators of the matrix proteolysis cascade and as an activator of plasminogen and hepatocyte growth factor (HGF), we studied matrix degradation in liver shortly after partial hepatectomy. The activation of plasminogen to plasmin following partial hepatectomy was examined by Western blot analysis, and a small increase in plasmin at approximately 15 minutes followed by a large elevation at approximately 3 to 6 hours after partial hepatectomy was detected. In addition, we found that fibrinogen, the major substrate for plasmin, begins to be degraded at approximately 15 to 30 minutes following partial hepatectomy. Using immunohistochemical staining, we detected that the distribution of fibrinogen in normal liver is localized to the perisinusoidal space surrounding the periportal region. A decreased distribution of fibrinogen in the periportal region was found by 15 minutes and continued through 24 hours following partial hepatectomy. In addition, the distribution of fibronectin in normal liver was localized to the perisinusoidal space surrounding the periportal and the pericentral regions. A strikingly decreased distribution of fibronectin in the periportal region was found at 5 minutes after partial hepatectomy. Furthermore, we observed that the protein levels of laminin, entactin, and fibronectin in an extracellular matrix (ECM)-enriched preparation decreased shortly after partial hepatectomy, and were restored later. No changes were observed with either vitronectin or the integrin chain α(v). In contrast to the protein levels of the ECM components, the messenger RNA (mRNA) levels of fibronectin, integrin chain β1, and integrin chain αv gradually increased over 18 hours and then decreased thereafter. Taken together, these results suggest that rapid reorganization of selected ECM components are important for hepatocyte proliferation at the early stages of liver regeneration.
Role of the Occluding Loop in Cathepsin B Activity (1997)

Within the lysosomal cysteine protease family, cathepsin B is unique due to its ability to act both as an endopeptidase and a peptidyldipeptidase. This latter capacity to remove C-terminal dipeptides has been attributed to the presence of a 20-residue insertion, termed the occluding loop, that blocks the primed terminus of the active site cleft. Variants of human procathepsin B, where all or part of this element was deleted, were expressed in the yeast Pichia pastoris. A mutant, where the 12 central residues of the occluding loop were deleted, autoprocessed, albeit more slowly than the wild type proenzyme, to yield a mature form of the enzyme with endopeptidase activity comparable with the wild-type cathepsin B, but totally lacking exopeptidase activity. This deletion mutant showed a 40-fold higher affinity for the inhibitor cystatin C, suggesting that the occluding loop normally restricts access of this inhibitor to the active site. In addition, the binding affinity of the cathepsin B propeptide, which is a potent inhibitor of this enzyme, was 50-fold increased, consistent with the finding that the loop reorients on activation of the proenzyme. These results suggest that the endopeptidase activity of cathepsin B is an evolutionary remnant since, as a consequence of its membership in the papain family, the propeptide must be able to bind unobstructed through the full length of the active site cleft.
Internal transcriptional regulatory elements in HIV-1 and other retroviruses. (1995)

The transcriptional regulation of retroviruses plays an important role in their pathogenesis. Cis-acting elements have been identified in the long terminal repeat (LTR) at the 5' extremity of the integrated provirus. These elements determine the rate and the site of transcription initiation and consist of arrays of binding sites for transcription factors. Recent studies have demonstrated the presence of additional regulatory elements, located outside of the LTR, within the transcribed region of several retroviruses including avian and murine retroviruses, HIV-1, HTLV-1 and the human spumaretroviruses. This review describes these new observations and analyzes their significance both in terms of retroviral transcriptional regulation and in terms of pathogenesis.
An evolutionary approach to training feedforward and recurrent neural networks (2002)

This paper describes a method of utilising genetic algorithms to train fixed architecture feedforward and recurrent neural networks. The technique described uses the genetic algorithm to evolve changes to the weights and biases of the network rather than the weights and biases themselves. Results achieved by this technique indicate that for many problems it compares very favourably with the more common gradient descent techniques for training neural networks, and in some cases is superior. The technique is useful for those problem which are known to be difficult for the gradient descent techniques.
Predictive animal testing for photocontact allergenicity (1980)

The purpose of this investigation was to establish a standardized animal model to predict the photoallergenic potential of new chemical compounds. In a first series of experiments the main factors influencing the induction of photoallergenicity were evaluated (induction concentration, pH of the test solution, pretreatment of the irradiation site with sodium lauryl sulphate, additional use of adjuvant injections and routes of administration). Osram Ultravitalux lamps were utilized for these studies. In a second series of experiments a Xenon 6000 W radiation source was used. Positive results were obtained with well known photosensitizers, as, for instance, the halogenated salicylanilides, as well as with so-called weak photoallergens (e.g. bithionol, sulphanilamide) by stimulating the animals' immune system with Freund's complete adjuvant. The photoallergenic compounds were at the same time tested for their contact allergenic potential in the optimization test. A standard procedure for the predictive photoallergenicity assay in guinea-pigs is proposed.
Principle of ferroelectric domain imaging using atomic force microscope (2001)

The contrast mechanisms of domain imaging experiments assisted by atomic force microscope (AFM) have been investigated by model experiments on nonpiezoelectric (silicon oxide) and piezoelectric [Pb(Zr,Ti)O3] thin films. The first step was to identify the electrostatic charge effects between the tip, the cantilever, and the sample surface. The second step was to explore the tip–sample piezoelectric force interaction. The static deflection of the cantilever was measured as a function of dc bias voltage (Vdc) applied to the bottom electrode (n-type Si wafers) for noncontact and contact modes. In addition, a small ac voltage (Vac sin ωt) was applied to the tip to measure the amplitude (Aω) and phase (Φω) of the first harmonic (ω) signal as a function of Vdc. By changing from the noncontact to the contact mode, a repulsive contribution to the static deflection was found in addition to the attractive one and a 180° phase shift in Φω was observed. These results imply that in the contact mode the cantilever buckling is induced by the capacitive force between the cantilever and the sample surface. This interaction adds to the tip–sample piezoelectric interaction thereby overlapping the obtained tip vibration signal. Therefore, the antiparallel ferroelectric domain images obtained at zero dc bias voltage will show a variation in Aω but a negligible one in Φω. The capacitive force contribution to the tip vibration signal was further verified in piezoelectric hysteresis loop measurement assisted by the AFM. The observed vertical offset of the loops was explained by the contact potential difference between the cantilever and the bottom electrode. The shape of the curve could be explained by the capacitive force interaction combined with the tip–sample piezoelectric interaction. The experimental results obtained in this study support the interpretation of the cantilever–sample capacitive force contribution to the tip vibration signal in ferroelectric domain imaging experiments using AFM as a probing tool. The use of a large area top electrode between the tip and the sample resulted in the elimination of the electrostatic cantilever–sample interaction with negligible degradation of the domain contrast. This method proved to be successful because the cantilever–sample interaction was hardly detected and only the tip–sample interaction was observed.
Organizing for East Asian Studies in the United States: The Origins of the Council on East Asian Libraries, Assocation for Asian Studies (1996)

The development of East Asian studies in the United States is basically a post-World War II phenomenon. Although a few universities offered some courses on East Asia (then referred to as the Far East) before World War II, fXl-fledged study of East Asia, in all the disciplines in the humanities and social sciences, did not develop until after the end of the Second World War. The war in the Pacific, the transformation of Japan into a democracy, the communist revolution in China, and the Korean War contributed to a heightening of the American awareness of the importance of East Asia in a changing world, and of the need for better understanding of their histories and civilizations. The universities, with generous foundation and government support, responded by expanding their teaching and research programs on East Asia, and today, after fifty years, East Asian studies in the United States is probably the largest and the most comprehensive in the Western world.
The battle for urban intelligence (2012)

(2012). The battle for urban intelligence. Construction Research and Innovation: Vol. 3, No. 3, pp. 14-17.
Synthesis of Lignin-Based Thermoplastic Copolyester Using Kraft Lignin as a Macromonomer (2009)

Lignin-based thermoplastic copolyester was synthesized for eco-friendly polymers and composite applications using lignin as a macromonomer to form a high molecular weight polymer. Kraft lignin was polymerized with sebacoyl chloride in the presence of triethylamine in N,N-dimethylacetamide (DMAc), and the molecular weight of the synthesized polymer was controlled by the polymerization temperatures and [COCl]/[OH] ratios providing up to 39 000 corresponding to 4–5 repeating units of lignin macromonomers. The glass transition temperature of the synthesized polymer was difficult to measure due to the random distribution of functional groups and irregular configurational or conformational arrangement of natural lignin. Therefore, the complex electric modulus (CEM) technique was used to determine the glass transition of the synthesized polymer to give around 70°C measured by the peak of the imaginary part of CEM. The synthesized lignin-copolyester exhibited good thermal stability up to 200°C in TGA analysis and, thus, it was possible to shape the synthesized polymer using the solvent casting or hot-melt processing techniques at 120°C–140°C without generating odor, fume or irritation. Although the molecular weight should further be increased in the future, the developed methodology may help to exploit new applications for eco-friendly sustainable materials in various fields.
Hypomagnesaemia due to use of proton pump inhibitors--a review. (2009)

Magnesium homeostasis is essential for many intracellular processes and depends on the balance of intestinal absorption and renal excretion. Hypomagnesaemia may arise from various disorders. We review the literature on hypomagnesaemia due to the use of proton pump inhibitors, as illustrated by a case of a 76-year-old woman with muscle cramps and lethargy caused by hypomagnesaemia and hypocalcaemia with a low parathyroid hormone level while using esomeprazole, a proton pump inhibitor (PPI). After oral magnesium repletion both abnormalities resolved. Fractional magnesium excretion was low, excluding excessive renal loss. A causal relation with PPI use was supported by the recurrence of hypomagnesaemia after rechallenge. In the past decade our understanding of transcellular magnesium transport was enhanced by the discovery of several gene mutations i.e. transient receptor potential melastin (TR PM) 6 and 7. In this light we discuss the possible aetiology of proton pump inhibitor related hypomagnesaemia.
Application of neural networks to inverse problems in electromagnetics (1994)

The paper presents a neural network approach for solving inverse problems in electromagnetics. In general, the measurements of the scattered electromagnetic fields can be related to the properties of the scatterer through integral equations. The energy minimization property of Hopfield neural networks is exploited to solve these integral equations. Results of implementing the method on an application problem involving reconstruction of material properties of multilayered media are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Receptor Signaling Clusters in the Immune Synapse (2012)

Signaling processes between various immune cells involve large-scale spatial reorganization of receptors and signaling molecules within the cell-cell junction. These structures, now collectively referred to as immune synapses, interleave physical and mechanical processes with the cascades of chemical reactions that constitute signal transduction systems. Molecular level clustering, spatial exclusion, and long-range directed transport are all emerging as key regulatory mechanisms. The study of these processes is drawing researchers from physical sciences to join the effort and represents a rapidly growing branch of biophysical chemistry. Recent advances in physical and quantitative analyses of signaling within the immune synapses are reviewed here.
Tissue-Engineered Follicles Produce Live, Fertile Offspring (2006)

Oocytes grown in vitro are of low quality and yield few live births, thus limiting the ability to store or bank the ova of women wishing to preserve their fertility. We applied tissue engineering principles to the culture of immature mouse follicles by designing an alginate hydrogel matrix to maintain the oocyte's 3- dimensional (3D) architecture and cell-cell interactions in vitro. A 3D culture mimics the in vivo follicle environment, and hydrogel-encapsulated follicles develop mature oocytes within the capacity for fertilization similar to that of oocytes matured in vivo. Embryos derived from cultured oocytes fertilized in vitro and transferred to pseudopregnant female mice were viable, and both male and female offspring were fertile. Our results demonstrate that alginate hydrogel-based 3D in vitro culture of follicles permits normal growth and development of follicles and oocytes. This system creates new opportunities for discovery in follicle biology and establishes a core technology for human egg banks for preservation of fertility.