gebhart/patrepeval huggingface dataset:
Acid-base transport by the renal proximal tubule (2010)

Each day, the kidneys filter 180 L of blood plasma, equating to some 4,300 mmol of the major blood buffer, bicarbonate (HCO3-). The glomerular filtrate enters the lumen of the proximal tubule (PT), and the majority of filtered HCO3- is reclaimed along the early (S1) and convoluted (S2) portions of the PT in a manner coupled to the secretion of H+ into the lumen. The PT also uses the secreted H+ to titrate non-HCO3- buffers in the lumen, in the process creating "new HCO3-" for transport into the blood. Thus, the PT - along with more distal renal segments - is largely responsible for regulating plasma [HCO3-]. In this review we first focus on the milestone discoveries over the past 50+ years that define the mechanism and regulation of acid-base transport by the proximal tubule. Further on in the review, we will summarize research still in progress from our laboratory, work that addresses the problem of how the PT is able to finely adapt to acid-base disturbances by rapidly sensing changes in basolateral levels of HCO3- and CO2 (but not pH), and thereby to exert tight control over the acid-base composition of the blood plasma.
Vector-based natural language call routing (1999)

This paper describes a domain-independent, automatically trained natural language call router for directing incoming calls in a call center. Our call router directs customer calls based on their response to an open-ended How may I direct your call? prompt. Routing behavior is trained from a corpus of transcribed and hand-routed calls and then carried out using vectorbased information retrieval techniques. Terms consist of n-gram sequences of morphologically reduced content words, while documents representing routing destinations consist of weighted term frequencies derived from calls to that destination in the training corpus. Based on the statistical discriminating power of the n-gram terms extracted from the caller&apos;s request, the caller is 1) routed to the appropriate destination, 2) transferred to a human operator, or 3) asked a disambiguation question. In the last case, the system dynamically generates queries tailored to the caller&apos;s request and the destinations with which it is consistent, based on our extension of the vector model. Evaluation of the call router performance over a financial services call center using both accurate transcriptions of calls and fairly noisy speech recognizer output demonstrated robustness in the face of speech recognition errors. More specifically, using accurate transcriptions of speech input, our system correctly routed 93.8% of the calls after redirecting 10.2% of all calls to a human operator. Using speech recognizer output with a 23% error rate reduced the number of correctly routed calls by 4%
Recombinant glycosyl-phosphatidylinositol-anchored proteins are not associated with protein kinases in transfected thymoma cells (1994)

The cross-linking by antibody of some glycosyl-phosphatidyl-inositol (GPI)-anchored proteins on the plasma membrane of T cells leads to cell activation. Phosphorylation of proteins on tyrosine residues has a central role in the control of T cell activation, and non-receptor protein tyrosine kinases can be coprecipitated with immune complexes of GPI-anchored proteins in T cell lysates. In order to investigate the nature of this interaction, two recombinant GPI-anchored proteins were constructed (using the GPI signal sequence from Thy-1), and their associations with protein tyrosine kinases in stable transfectants of a mouse thymoma have been investigated. One recombinant GPI protein is the extracellular domain of the human complement receptor-1, normally an integral membrane protein, and the other is the secreted protein, human tissue inhibitor of metalloproteinases. The latter protein should be foreign to the cell surface and yet has been expressed as a GPI-anchored protein at levels equivalent to the highly expressed antigens Thy-1 and Ly6.A2 on mouse thymoma cells. Neither of the two recombinant proteins, when immunoprecipitated from NP40 lysates of transfected cells, was associated with protein tyrosine kinases in contrast with the natural endogenous GPI-anchored proteins Thy-1 and Ly6.A2 in non-transfected parental cells. Moreover, high expression of foreign recombinant GPI protein appears to interfere with the association of the natural GPI proteins with protein tyrosine kinases.
A temperature stabilized RF detector with extended dynamic range (1982)

The purpose of this paper is to document some of the finer points which became apparent during the development of an RF powermeter. The powermeter, intended for use in a hostile thermal environment, was an integral part of an automated test set used to evaluate mobile telephone units. The initial task was to develop circuitry that produced a DC output voltage which was simply related to the RF input power. The circuit performance was further specified to accommodate a wide dynamic range of inputs and to remain reasonably accurate despite wide temperature variations. The development was begun by employing DC current biasing to improve the detector's sensitivity to low level input signals. Next a subtractive technique was utilized to provide improved temperature stability. An additive technique was devised to extend the range of linear operation. Only by employing all of these methods was the resultant circuit able to meet its requirements. In the sections which follow, the current biased envelope detector with the proposed improvements is discussed, a circuit is introduced, and experimental results which confirm the validity of the suggested techniques are presented.
Using an Inverse PCR Strategy to Clone Large, Contiguous Genomic DNA Fragments (2003)

Conventional PCR screens of genomic DNA will often yield a substantial fragment of the gene of interest. However, identification of flanking sequences on either side of a known sequence can be problematic with conventional PCR. in which primers extend a complementary chain in a 5′ → 3′ direction. However, if the template DNA is circularized and then used with primers that are oriented with their 3′ ends directed away from each other, amplification around the circular template results in a linear PCR product consisting of uncharacterized DNA fragments flanked by the known DNA sequences (Fig. 1). This variation of the conventional PCR strategy is known as inverse PCR (1,2). and we have used the technique to amplify myosin sequences in Tetrahymena (3). In this chapter we describe protocols that enable the investigator to apply the inverse PCR technique to clone contiguous sequences upstream and downstream of a known DNA sequence.
Revealing In-Stent Stenoses of the Iliac Arteries: Comparison of Multidetector CT with MR Angiography and Digital Radiographic Angiography in a Phantom Model (2002)

CT angiography is suited for detection of relevant stenoses in steel, cobalt-based, and nitinol stents. MR angiography is superior only in tantalum products.
Synthesis of Stable and Cell-type Selective Analogues of Cyclic ADP−Ribose, a Ca<sup>2+</sup>-Mobilizing Second Messenger. Structure−Activity Relationship of the N1-Ribose Moiety<sup>1</sup> (2005)

We previously developed cyclic ADP-carbocyclic ribose (cADPcR, 2) as a stable mimic of cyclic ADP-ribose (cADPR, 1), a Ca(2+)-mobilizing second messenger. A series of the N1-ribose modified cADPcR analogues, designed as novel stable mimics of cADPR, which were the 2"-deoxy analogue 3, the 3"-deoxy analogue 4, the 3"-deoxy-2"-O-(methoxymethyl) analogue 5, the 3"-O-methyl analogue 6, the 2",3"-dideoxy analogue 7, and the 2",3"-dideoxydidehydro analogue 8, were successfully synthesized using the key intramolecular condensation reaction with phenylthiophosphate-type substrates. We investigated the conformations of these analogues and of cADPR and found that steric repulsion between both the adenine and N9-ribose moieties and between the adenine and N1-ribose moieties was a determinant of the conformation. The Ca(2+)-mobilizing effects were evaluated systematically using three different biological systems, i.e., sea urchin eggs, NG108-15 neuronal cells, and Jurkat T-lymphocytes. The relative potency of Ca(2+)-mobilization by these cADPR analogues varies depending on the cell-type used: e.g., 3"-deoxy-cADPcR (4) > cADPcR (2) > cADPR (1) in sea urchin eggs; cADPR (1) >> cADPcR (2) approximately 3"-deoxy-cADPcR (4) in T-cells; and cADPcR (2) > cADPR (1) > 3"-deoxy-cADPcR (4) in neuronal cells, respectively. These indicated that the target proteins and/or the mechanism of action of cADPR in sea urchin eggs, T-cells, and neuronal cells are different. Thus, this study represents an entry to cell-type selective cADPR analogues, which can be used as biological tools and/or novel drug leads.
CXLVIII.—Organic ferric salts (1913)

S. U. Pickering, J. Chem. Soc., Trans., 1913, 103, 1358 DOI: 10.1039/CT9130301358
New nonlinear optical crystal K_2Al_2B_2O_7 (2000)

The new nonlinear optical crystal K2Al2B2O7 is discovered with the molecular engineering approach on the basis of anionic group theory. An optically perfect single crystal with space group P321, free of moisture and hygroscopy, is readily grown by the top-seeding flux method. Its transparence range covers 180 to 3600 nm. The refractive indices are measured with the minimum-deviation method, based on which the Sellmeier equation is obtained. The measured nonlinear optical coefficient d11 is 0.45 pm/V. The moderate walk-off angle and angular bandwidth, together with the high optical homogeneity, make it a promising candidate for the fourth- and the fifth-harmonic generation of a Nd:YAG laser.
Bio-inspired 3D microenvironments: a new dimension in tissue engineering (2016)

Biomaterial scaffolds have been a foundational element of the tissue engineering paradigm since the inception of the field. Over the years there has been a progressive move toward the rational design and fabrication of bio-inspired materials that mimic the composition as well as the architecture and 3D structure of tissues. In this review, we chronicle advances in the field that address key challenges in tissue engineering as well as some emerging applications. Specifically, a summary of the materials and chemistries used to engineer bio-inspired 3D matrices that mimic numerous aspects of the extracellular matrix is provided, along with an overview of bioprinting, an additive manufacturing approach, for the fabrication of engineered tissues with precisely controlled 3D structures and architectures. To emphasize the potential clinical impact of the bio-inspired paradigm in biomaterials engineering, some applications of bio-inspired matrices are discussed in the context of translational tissue engineering. However, focus is also given to recent advances in the use of engineered 3D cellular microenvironments for fundamental studies in cell biology, including photoresponsive systems that are shedding new light on how matrix properties influence cell phenotype and function. In an outlook for future work, the need for high-throughput methods both for screening and fabrication is highlighted. Finally, microscale organ-on-a-chip technologies are highlighted as a promising area for future investment in the application of bio-inspired microenvironments.
How Sexual Abuse Interviews Go Astray: Implications for Prosecutors, Police, and Child Protection Services (2000)

This article argues that child sexual abuse interviews can go astray in two different ways: (a) improper interviewing has the potential to elicit false allegations from children, and (b) clumsy interviewing does not typically produce false allegations, but may have other negative consequences, particularly for child victims. The article clarifies the distinction between the two kinds of bad interviewing and suggests that clumsy interviewing is the more common of the two. The potential negative consequences of both improper and clumsy interviewing are described, along with implications for prosecutors, police, and child protection services. In the authors' opinion, improper interviewing can probably be eliminated rather easily, but clumsy interviewing may be considerably more resistant to change.
Mechanical properties of a discontinuous random fiber composite for totally bioabsorbable fracture fixation devices (2002)

The mechanical properties of a new class of bioabsorbable polymer/composite based on the amino acid tyrosine and calcium phosphate fibers were examined. The tensile modulus of the neat polymer was increased by more than 115% by using a plasma fiber treatment. The use of these innovative materials in fixation devices could potentially eliminate the need for a second surgery to retrieve the implant.
Neighbor discovery and resource allocation for device-to-device communication (2014)

Device-to-Device (D2D) communication has attracted lots of attention as one of the most advanced wirelesscommunication technologies which allows access to services offered by nearby devices bypassing the BaseStation (BS). The potential advantages of this direct communication paradigm include high data rate, networkoffloading and range extension, as well as commercial proximity services and social networking. From the UserEquipments (UEs) and BS perspective, additional protocol overhead and discovery resource are required forD2D links. In such a context, neighbor discovery and resource allocation approaches need to be studied. For anefficient D2D communication, the main problem is how the UEs in proximity detect each other and establish aD2D link in a timely and efficient manner. In this thesis we investigate D2D-enabled cellular network and westudy neighbor discovery and resource allocation in such network. We split the cell into two parts: the inner partin which UEs communicate via BS and the outer part where UEs use D2D links as a means of communication.The blocking probability for these two parts is calculated based on Poisson and Engset distributions. Wepropose two protocols for neighbor discovery, namely, reactive (on-demand) discovery and proactive (multicast)discovery and both of them are infrastructure-coordinated protocols. The control overhead is calculated andnumerical results are provided based on three cases of D2D pair requests in different timeslots in order tocompare these two protocols. The performance evaluation and results show that the reactive protocolperforms better when the D2D communication traffic load is low whereas proactive protocol is preferable ifD2D communication demand is high. If the overflowed UEs in proximity are allowed to discover each otherusing our protocols together with dedicated resource from the BS and communicate via D2D links; results showthat the cellular network blocking probability is reduced.Keywords: Device-to-Device communication, ProSe discovery, protocol design, control overhead, performancecomparison.
Functional and high level expression of human dopamine beta-hydroxylase in transgenic mice. (1994)

Dopamine beta-hydroxylase (DBH; EC 1.14.17.1) catalyzes the production of the neurotransmitter and hormone norepinephrine in the third step of the catecholamine biosynthesis pathway. Transgenic mice were generated with multiple copies of a human DBH minigene construct containing the full-length cDNA connected downstream of the 4-kilobase upstream promoter region to achieve overexpression of DBH. Human DBH mRNA and immunoreactivity were detected tissue-specifically in the brain and adrenal gland of these transgenic mice. The transgene products were correctly processed to a glycosylated mature polypeptide with a molecular mass of 72 kDa and existed in the secretory vesicles as both soluble and membrane-bound forms. We detected a marked increase in DBH activity in various catecholamine-containing tissues of the mice that occurred as a consequence of expression of the catalytically active human DBH enzyme. However, in these transgenics the steady-state levels of norepinephrine and epinephrine were normally maintained without the acceleration of the catecholamine turnover rate, suggesting that there are some regulatory mechanisms to preserve a constant rate of norepinephrine synthesis in spite of the increased amount of DBH protein. These transgenic mice with the minigene construct provide one approach to study the mechanisms underlying biogenesis of the DBH polypeptide and regulation of norepinephrine synthesis.
Object representatives: a uniform abstraction for pointer information (2008)

Pointer analyses enable many subsequent program analyses and transformations by statically disambiguating references to the heap. However, different client analyses may have different sets of pointer analysis needs, and each must pick some pointer analysis along the cost/precision spectrum to meet those needs. Some analysis clients employ combinations of pointer analyses to obtain better precision with reduced analysis times. Our goal is to ease the task of developing client analyses by enabling composition and substitutability for pointer analyses. We therefore propose object representatives, which statically represent runtime objects. A representative encapsulates the notion of object identity, as observed through the representative’s aliasing relations with other representatives. Object representatives enable pointer analysis clients to disambiguate references to the heap in a uniform yet flexible way. Representatives can be generated from many combinations of pointer analyses, and pointer analyses can be freely exchanged and combined without changing client code. We believe that the use of object representatives brings many software engineering benefits to compiler implementations because, at compile time, object representatives are Java objects. We discuss our motivating case for object representatives, namely, the development of an abstract interpreter for tracematches, a language feature for runtime monitoring. We explain one particular algorithm for computing object representatives which combines flow- sensitive intraprocedural must-alias and must-not-alias analyses with a flow-insensitive, context-sensitive whole-program points-to analysis. In our experience, client analysis implementations can almost directly substitute object representatives for runtime objects, simplifying the design and implementation of such analyses.
Selecting Lysine-Excreting Mutants of Lactobacilli for Use in Food and Feed Enrichment (1974)

Lysine analogues are used to select for lysine-excreting mutants of Lactobacillus plantarum. The use of lactobacilli that excrete lysine for the enrichment of foods and feedstuffs by fermentation is discussed. The increase in lysine content of soybean milk by a mutant of L. bulgaricus and in silage by L. plantarum is shown.
Fast Mode Decision Algorithm for Intra Prediction in H.264/AVC (2006)

In H.264/AVC, a novel criterion named the rate distortion optimization (RDO) is employed to select the optimal coding modes for each macroblock (MB) within the intra prediction coding pictures, which can achieve a high compression ratio while leading to a great increase in the complexity and computational load unfortunately. In this paper, a fast mode decision algorithm based on integer transform and adaptive threshold is proposed. Before the intra prediction, integer transform operations on the original image are executed to find the directions of local textures. According to this direction, only a small part of the possible intra prediction modes are tested at the first step. If the summation of differences (SAD) of the reconstructed block corresponding to the best mode is smaller than an adaptive threshold, calculation is terminated. Otherwise, more possible modes are needed. Simulations show that the fast mode decision algorithm proposed in this paper can accelerate the speed of intra picture coding significantly only with a negligible PSNR loss or a bit rate increment.
Denial-of-App Attack (2014)

We describe a novel class of attacks called denial-of-app that allows adversaries to inhibit the future installation of attacker-selected applications on mobile phones. Adversaries can use such attacks to entrap users into installing attacker-preferred applications, for instance to generate additional revenue from advertisements on a competitive app market or to increase the rate of malware installation. Another possibility is to block anti-virus applications or security workarounds to complicate malware detection and removal.
On the dielectric properties and normalized radar cross-section of crude oil-contaminated sea ice (2017)

This thesis explores the effects of crude oil spilled beneath young sea ice on the dielectric properties and normalized radar cross-section of the ice at microwave (C-band) frequencies. The dielectric profile, also referred to as the complex permittivity profile, of sea ice is a governing factor in how the ice scatters incident electromagnetic waves, thus affecting its associated normalized radar cross-section. The dielectric profile of sea ice is dependent on both the geophysical and thermal properties of the ice. Crude oil contained beneath, within, or on the surface of young sea ice was expected to change these properties, thus impacting both the dielectric profile and normalized radar cross-section of the ice. Differences between the dielectric profile and normalized radar cross-section of uncontaminated and oil-contaminated sea ice is expected to facilitate detection of oil-contaminated sea ice through active microwave remote sensing technologies. As such, a discussion of the geophysical, thermodynamic, and electromagnetic properties of sea ice is presented, as well as an overview of the behaviour of oil in ice infested environments and the efforts undertaken to detect crude oil-contaminated sea ice. Following this, the details of a preliminary laboratory experiment conducted to explore the differences in the dielectric profiles of uncontaminated and contaminated sea ice are presented. Next, a comprehensive description of the meso-scale crude oil-in-sea ice experiment and the results, including the modelled dielectric profiles and measured normalized radar cross-sections of uncontaminated and oil-contaminated sea ice, is provided. Finally, a simulation study comparing the normalized radar cross-section for the uncontaminated and oil-contaminated cases is presented. Based on the experimental and simulation work conducted, the observed differences in the temperature profiles and normalized radar cross-sections of uncontaminated and oil-contaminated sea ice suggest that differentiation between uncontaminated and oil-contaminated young sea ice using microwave remote sensing technologies may be possible.
Molecular characterization of prostatic small‐cell neuroendocrine carcinoma (2003)

Prostate small cell carcinoma expresses a diverse repertoire of genes that reflect characteristics of their NE cell of origin. ASCL1, INA, and SV2B are potential molecular markers for small cell NE tumors and NE cells of the prostate. This small cell NE carcinoma gene expression profile may yield insights into the development, progression, and treatment of subtypes of prostate cancer.
X-ray structure of a biantennary octasaccharide-lectin complex refined at 2.3-A resolution. (1992)

The structure and flexibility of saccharides have a profound and specific influence in several biological processes such as protein protection and the maintenance of conformational integrity, and in recognition events involving viruses, enzymes, and lectins. To establish the structural bases of these phenomena, we describe herein the extensively refined 2.3-A resolution x-ray structure of a biantennary octasaccharide of the N-acetyllactosamine type, complexed to isolectin I from Lathyrus ochrus. The two octasaccharides are located in clefts at each end of the long axis of the lectin. The conformations of both the lectin and the saccharide are slightly modified upon binding. The complex is stabilized by numerous hydrogen bonds, many of them involving water molecules. It is also stabilized by van der Waals interactions, including some with aromatic residues. A more general model of a possible lectin-glycoprotein interaction is also proposed.