gebhart/patrepeval huggingface dataset:
Nutritional and endocrinological influences on the composition of animal growth. (1987)

Several domesticated species of mammals are raised to provide protein for human consumption. The goal of producers is to generate a product, lean meat, efficiently. Much of the weight gain of animals is fat, a large portion of which is not needed by the animal and unwanted by the human consumer. Thus, improvement in efficiency of animal growth must consider not only rate of weight gain and use of feed to support the gain but also the composition of the gain. One method to improve efficiency of growth, including body composition is to lower the energy intake of animals; feeding less than ad libitum is particularly effective for some species. There are three types of endocrines, anabolic steroids, growth hormone and adrenergic agonists, that have demonstrated ability to change mammalian growth and body composition. Exogenous anabolic steroids increase weight gain, improve efficiency of feed utilization and change body composition toward more muscle and less fat. They are especially effective in ruminant species and are used in beef cattle. Exogenous growth hormone has the same effects as anabolic steroids but is effective in nonruminant species as well. Exogenous adrenergic agonists, analogs of norepinephrine, have marginal effects on weight gain and feed efficiency but favorably change body composition in all species. As more is understood about the control of endocrine secretion, the possibility arises for animal manipulation by administration of exogenous releasing factors or release-inhibiting factors or by changing central nervous system neurotransmitter control of the hypothalamic production and release of these factors. It is also possible to use selective immunization to modify endogenous hormones. Thus, biological knowledge coupled with modern technology continues to open many frontiers to favorably change animal growth and composition. Some of these approaches are in use, several are in experimental use and others await experimental demonstration of utility.
Parfait - A Scalable Bug Checker for C Code (2008)

Parfait is a bug checker of C code that has been designed to address developers' requirements of scalability (support millions of lines of code in a reasonable amount of time), precision (report few false positives) and reporting of bugs that may be exploitable from a security vulnerability point of view. For large code bases, performance is at stake if the bug checking tool is to be integrated into the software development process, and so is precision, as each false alarm (i.e., false positive) costs developer time to track down. Further, false negatives give a false sense of security to developers and testers, as it is not obvious or clear what other bugs were not reported by the tool. A common criticism of existing bug checking tools is the lack of reported metrics on the use of the tool. To a developer it is unclear how accurate the tool is, how many bugs it does not find, how many bugs get reported that are not actual bugs, whether the tool understands when a bug has been fixed, and what the performance is for the reported bugs. In this tool demonstration we show how Parfait fairs in the area of buffer overflow checking against the various requirements of scalability and precision.
Induction of follicle formation and hair growth by vibrissa dermal papillae implanted into rat ear wounds: vibrissa-type fibres are specified (1992)

Adult vibrissa follicle dermal papillae have the capacity to induce hair growth and follicle formation when associated with epidermis from various sources. However, the range of conditions under which hair follicle induction will take place has not been established. The question of whether or not the adult papilla carries information to impose fibre-type specificity has also not been fully answered. This study describes how the implantation of isolated papillae into small incisional cuts on the rat ear pinna resulted in the subsequent emergence of abnormally large hair fibres from the wound sites. Many of these hairs were found to display vibrissa-type characteristics. Histological observations indicated that the papillae had interacted with the edges of the wound epidermis to produce new, and particularly large follicles, while immunohistochemical staining revealed that early follicle construction was accompanied by a profusion of the basement membrane constituents laminin and type IV collagen in the subjacent dermis. These findings show that adult rat papillae retain the capacity, as displayed by embryonic dermis, to determine vibrissa specificity in induced follicles.
Surfactant polymers designed to suppress bacterial (Staphylococcus epidermidis) adhesion on biomaterials (2000)

We describe a series of surfactant polymers designed as surface-modifying agents for the suppression of bacterial adhesion on biomaterials. The surfactant polymers consist of a poly(vinyl amine) backbone with hydrophilic poly(ethylene oxide) (PEO) and hydrophobic hexanal (Hex) side chains (PVAm/PEO:Hex). Surface modification is accomplished by simple dip coating from aqueous solution, from which surfactant polymers undergo spontaneous surface-induced assembly on hydrophobic biomaterials. The stability of PVAm/PEO:Hex on pyrolytic graphite (HOPG) and polyethylene (PE) was demonstrated by the absence of detectable desorption under flow conditions of pure water over a 24-h period. PEO surfactant polymers with four different PEO:Hex ratios (1:1.4, 1:2.5, 1:4.6, and 1:10.7) and a dextran surfactant polymer were compared with respect to S. epidermidis adhesion under dynamic flow conditions. Suppression of S. epidermidis adhesion was achieved for all modified surfaces over the shear range 0-15 dyn/cm(2). The effectiveness depended on the surfactant polymer composition such that S. epidermidis adhesion to modified surfaces decreased significantly with increasing PEO packing density. Modified HOPG was more effective in reducing bacterial adhesion compared with the corresponding modification on PE, which we attribute to the presence of defects in surfactant polymer assembly on PE. Our results are discussed from the perspective of critical factors, such as optimal PEO packing density and hydration thickness, that contribute to the effectiveness of surfactant polymers to shield a biomaterial from adhesive bacterial interactions.
Molecular requirement for interleukin 1 induction by lipopolysaccharide‐stimulated human monocytes: Involvement of the heptosyl‐2‐keto 3‐deoxyoctulosonate region (1986)

Experiments were undertaken to localize in the lipopolysaccharide (LPS) the minimal structural determinants sufficient to initiate the signal leading to interleukin 1 (IL 1) secretion by human monocytes. Our results clearly demonstrated that this signal is triggered by structures present in the so-called inner-core region which chemically consists of 2-keto-3-deoxy-D-manno-octulosonic acid (KDO) and heptose in many LPS of gram-negative bacteria. Thus, the isolated polysaccharide region of Bordetella pertussis endotoxin as well as fragments derived therefrom containing the reducing KDO unit were able to induce similar levels of IL1 induction as the native LPS. Similarly, the trisaccharide alpha-D-manno-heptopyranosyl-(1-3)-alpha-D-manno-heptopyranosyl -(1-5)-3 -deoxy-D-manno-octulosonic acid (hep-hep-KDO), representative for the inner-core region of a large number of enterobacterial LPS, was a very potent IL 1 inducer. Neither KDO monosaccharide, nor the alpha-(2-4)-linked 3-deoxy-D-manno-octulosonic acid disaccharide isolated from Salmonella rough-form LPS promoted the signal indicating that the minimal structure of endotoxin able to induce IL 1 secretion resides in the hep (1-5)-KDO disaccharide.
Light-Emitting Diodes as Sensors for Colorimetric Analyses (1997)

A new nondispersive colorimetric analyzer has been developed with the use of light-emitting diodes (LEDs) as optical sensors coupled to an artificial neural network (ANN). In this application, various colored LEDs are used as optical detectors with tuned bandpasses. The device has been evaluated against conventional spectrometric methods in the determination of pH and heavy metals by the use of colorimetric procedures. The spectrometer benefits from a simple design, ease of application, inexpensive cost of construction, and long life.
Accuracy and Resolution of Kinect Depth Data for Indoor Mapping Applications (2012)

Consumer-grade range cameras such as the Kinect sensor have the potential to be used in mapping applications where accuracy requirements are less strict. To realize this potential insight into the geometric quality of the data acquired by the sensor is essential. In this paper we discuss the calibration of the Kinect sensor, and provide an analysis of the accuracy and resolution of its depth data. Based on a mathematical model of depth measurement from disparity a theoretical error analysis is presented, which provides an insight into the factors influencing the accuracy of the data. Experimental results show that the random error of depth measurement increases with increasing distance to the sensor, and ranges from a few millimeters up to about 4 cm at the maximum range of the sensor. The quality of the data is also found to be influenced by the low resolution of the depth measurements.
Amino acid sequences of the two major isoforms of troponin C from crayfish (1989)

The primary structure of the two major isoforms (alpha and gamma) of troponin C (TnC) from crayfish tail muscle has been determined by the application of manual and automated Edman degradation procedures to fragments generated by suitable chemical and proteolytic cleavages. Both amino acid sequences commence with an acetylated methionyl residue and contain 150 amino acid residues, including a single proline residue at position 29 and 2 residues of tyrosine at positions 95 and 102. No cysteine or tryptophan are present. The molecular weights calculated for alpha- and gamma-TnC are 17,157 and 16,974, respectively. The two crayfish proteins are invariable at 129 positions and conserved at 11 others. Pairwise comparisons show that the two sequences are 33-39% identical with those of seven TnCs reported so far and 39% identical with that of bovine brain calmodulin. The N-terminal end of about 10 residues, found in vertebrate TnCs, is absent in crayfish TnCs. In the latter proteins, domains I and III appear as abortive Ca2+-binding sites due to nonconservative amino acid replacements at the key Ca2+-coordinating positions in their loops. The remaining two Ca2+-binding loops (II and IV) show a remarkable similarity with the Ca2+-specific loops (I and II) found in vertebrate TnCs. These findings are consistent with the Ca2+-binding data (Wnuk, W. (1989) J. Biol. Chem. 264, 18240-18246) which indicate the presence of two Ca2+-specific sites in crayfish TnCs. These two sites display the same affinity for Ca2+ (log KCa = 4.3) on gamma-TnC but differ in their affinity (log KCa = 6.0 and 4.1) on alpha-TnC. The only structural difference between the dodecapeptide loops II and IV in both alpha- and gamma-TnC, which correlates with the existence of the high affinity (log KCa = 6.0) Ca2+-specific site on alpha-TnC, is position 11 occupied by a methionyl residue in the loop IV of alpha-TnC as opposed to negatively charged residues found in the other three loops. This suggests that the high affinity Ca2+-specific site on alpha-TnC is located in domain IV. Since the Ca2+-binding studies show that the formation of the complex of crayfish troponin I (TnI) with alpha- and gamma-TnC increases significantly the affinity of only one of their two Ca2+-specific sites and this TnI-sensitive site is not the high affinity Ca2+-specific site on alpha-TnC, we conclude that the binding of Ca2+ to site II controls the Ca2+-dependent interaction between crayfish TnCs and TnI.
Perceptual “vowel spaces” of cochlear implant users: Implications for the study of auditory adaptation to spectral shift (2001)

Cochlear implant (CI) users differ in their ability to perceive and recognize speech sounds. Two possible reasons for such individual differences may lie in their ability to discriminate formant frequencies or to adapt to the spectrally shifted information presented by cochlear implants, a basalward shift related to the implant's depth of insertion in the cochlea. In the present study, we examined these two alternatives using a method-of-adjustment (MOA) procedure with 330 synthetic vowel stimuli varying in F1 and F2 that were arranged in a two-dimensional grid. Subjects were asked to label the synthetic stimuli that matched ten monophthongal vowels in visually presented words. Subjects then provided goodness ratings for the stimuli they had chosen. The subjects' responses to all ten vowels were used to construct individual perceptual "vowel spaces." If CI users fail to adapt completely to the basalward spectral shift, then the formant frequencies of their vowel categories should be shifted lower in both F1 and F2. However, with one exception, no systematic shifts were observed in the vowel spaces of CI users. Instead, the vowel spaces differed from one another in the relative size of their vowel categories. The results suggest that differences in formant frequency discrimination may account for the individual differences in vowel perception observed in cochlear implant users.
Effects of S -Nitrosation of Hemoglobin on Hypoxic Pulmonary Vasoconstriction and Nitric Oxide Flux (2001)

Free hemoglobin (Hb) augments hypoxic pulmonary vasoconstriction (HPV), ostensibly by scavenging nitric oxide (NO). However, recent evidence suggests that Hb that is S-nitrosated may act as an NO donor and vasodilator. We studied the effects of oxyHb, Hb that is chemically modified to prevent heme binding or oxidation of NO (cyanometHb), and Hb that is S-nitrosated (SNO-Hb and SNO-cyanometHb) on HPV, expired NO (eNO), and perfusate S-nitrosothiol (SNO) concentration in isolated, perfused rabbit lungs. Perfusate containing either 4 microM oxyHb or SNO-Hb increased normoxic pulmonary artery pressure (Ppa), augmented HPV dramatically, and resulted in an 80% fall in eNO in comparison to perfusion with buffer, whereas 4 microM cyanometHb or SNO-cynanometHb had no effect on these variables. Excess glutathione (GSH) added to perfusate containing SNO-Hb resulted in a 20 to 40% fall in the perfusate SNO concentration, with a concomitant increase in metHb content, without affecting Ppa, HPV, or eNO. In conclusion, free Hb augments HPV by scavenging NO, an effect that is not prevented by S-nitrosation. NO released from SNO-Hb in the presence of GSH does not produce measurable vascular effects in the lung or changes in eNO because of immediate oxidation and metHb formation.
Iron in Eutrophic Clear Lake, California: Its Importance for Algal Nitrogen Fixation and Growth (1983)

Clear Lake, California, is warm, shallow, polymictic, and eutrophic. During 1975, levels of dissolved (&lt; 0.45 μm) iron in all three basins of Clear Lake were always low (15–30 μg∙L −1 ) and decreased to 2 μg∙L −1 during the major bloom of Aphanizomenon flos-aquae. Nitrogen fixation (acetylene reduction) rates of the blue-green algal populations were stimulated as much as 500% above control levels by iron additions in laboratory and in situ large-volume bioassays. Carbon fixation rates and chlorophyll a levels were also significantly stimulated by iron additions, but usually less rapidly and to a lesser extent than N 2 fixation. Additions of nitrate stimulated carbon fixation and chlorophyll production but inhibited increases in nitrogen fixation. Phosphate additions either had no effect or produced a mixture of stimulation or depression of all three variables. The bioassays indicate that the growth of blue-green algae and other algae in Clear Lake is usually directly limited by combined nitrogen and occasionally by iron or phosphorus. Low iron levels aggravate the effects of low nitrogen by limiting nitrogen fixation, thus reducing blue-green algal growth.
Non-sticking drops (2005)

While the behaviour of large amounts of liquid is dictated by gravity, surface forces become dominant at small scales. They have for example the remarkable ability to make droplets stick to their substrates (even if they are inclined), which is a practical issue in many cases (windshields, window panes, greenhouses, or microfluidic devices). Here we describe how this problem can be overcome with super-hydrophobic materials. These materials are often developed thanks to micro-textures, which decorate a solid surface, and we describe the way such textures modify the wettability of that solid. We conclude by showing the unusual dynamics of drops in a super-hydrophobic situation.
Collaborative relevance judgment: A group consensus method for evaluating user search performance (2001)

Abstract Relevance judgment has traditionally been considered a personal and subjective matter. A user's search and the search result are treated as an isolated event. To consider the collaborative nature of information retrieval (IR) in a group/organization or even societal context, this article proposes a method that measures relevance based on group/peer consensus. The method can be used in IR experiments. In this method, the relevance of a document is decided by group consensus, or more specifically, by the number of users (or experiment participants) who retrieve it for the same search question. The more users who retrieve it, the more relevant the document will be considered. A user's search performance can be measured by a relevance score based on this notion. The article reports the results of an experiment using this method to compare the search performance of different types of users. Related issues with the method and future directions are also discussed.
T-Scan Electrical Impedance Imaging System for Anomaly Detection (2004)

We consider an inverse conductivity problem arising in anomaly detections with its mathematical model based on the T-Scan system (breast cancer detection system). In this model, we try to detect an anomaly D from one or two sets of measured data that are available only on a small portion $\Gamma$ of the boundary of the subject $\Omega$. In practice, $\Omega$ differs in each subject, so our detection algorithm should not depend much on the global geometry of $\Omega$. The purpose of this work is to provide a mathematical ground for the reconstruction of a rough feature of D which is stable against any measurement noise and any change of geometry $\partial\Omega$. Based on rigorous estimates with a simplified model, we found an approximation that gives a noniterative detection algorithm of finding a useful feature of anomaly. We also present a multifrequency approach to handling the case where the complex conductivity of the background is not homogeneous and is not known a priori.
Absorption of l-methionine from the human small intestine (1968)

Absorption of L-methionine was measured in all parts of the human small intestine using transintestinal intubation and perfusion. In four normal subjects, adsorption was higher in the proximal than in the distal intestine. In two patients with nontropical sprue in relapse, there was a proximal zone of low absorption with higher absorption distally. In all parts of the small intestine, absorption showed rate-limiting kinetics as methionine concentration was increased. In normal subjects, the proximal K(m) (Michaelis constant) was more than 3 times higher than the distal, which suggests a difference in transport mechanisms between the two segments.
Blockade of CD40-Mediated Signaling Is Sufficient for Inducing Islet But Not Skin Transplantation Tolerance (2003)

Treatment of mice with a single donor-specific transfusion (DST) plus a brief course of anti-CD154 mAb to block CD40-mediated signaling uniformly induces donor-specific transplantation tolerance. Survival of islet allografts in treated mice is permanent, but skin grafts eventually fail unless recipients are thymectomized. The nature of the cellular mechanisms involved and the basis for the difference in survival of islet vs skin allografts are not known. In this study, we used CD40 knockout mice to investigate the role of CD40-mediated signaling in each component of the tolerance induction protocol: the DST, the graft, and the host. When CD40-mediated signaling was eliminated in only the DST or the graft, islet allografts were rapidly rejected. However, when CD40 signaling was eliminated in the host, approximately 40% of the islet allografts survived. When CD40 signaling was eliminated in the DST, the graft, and the host, islet grafts survived long term (>84 days), whereas skin allografts were rapidly rejected ( approximately 13 days). We conclude that transplantation tolerance induction in mice treated with DST and anti-CD154 mAb requires blockade of CD40-mediated signaling in the DST, the graft, and the host. Blockade of CD40-mediated signaling is necessary and sufficient for inducing islet allograft tolerance and is necessary but not sufficient for long-term skin allograft survival. We speculate that a requirement for regulatory CD4(+) T cells in skin allograft recipients could account for this differential response to tolerance induction.
Purification of the TET repressor and TET operator from the transposon Tn10 and characterization of their interaction. (1982)

The TET repressor for the TnlO-encoded tetracycline resistance gene has been purified to near-homogeneity.The TET repressor binds ['Hltetracycline with an apparent association constant greater than lo7 litersmol-'.The formation of the TET repressor * tetracycline complex is optimal between pH 7.5 and pH 12 and is reduced below pH 7.5.At pH 5.0, the TET repressor is inactive.The thermal stability extends up to 55 "C and drops sharply to zero between 55 "C and 65 "C.Specific binding of the TET repressor to the TET operator is demonstrated by the protection of a single recognition site for the restriction endonuclease HincII out of two sites on the respective DNA fragment.This function of the TET repressor is inhibited in the presence of 4 PM tetracycline.The location of the operator is determined within 100 base pairs by the lack of protection of other restriction sites.The interaction of the TET repressor with the TET operator is characterized in vitro using short, homogeneous DNA fragments containing the "0-encoded TET gene control sequences, which were cloned under reconstruction of the Eco RI sites into pVH51.These fragments contain the TET gene control elements and different parts of flanking sequences.The 187-base pair (bp) fragment was prepared in milligram amounts from multiple insertion plasmids and radioactively labeled by filling in the protruding Eco RI ends using [%IATP.The TET repressor binds the 187-bp fragment with an apparent association constant greater than IO7 liters-mol".The stoichiometry is 4 TET repressor molecules/l87-bp DNA.A 300-fold molar excess of a 180-bp fragment prepared from a Hue III digest of pVH51 does not compete with the 187-bp DNA for TET repressor binding.This result is interpreted as specific interaction of the TET repressor with the TET operator in the 187-bp fragment.This specific interaction is inhibited in the presence of tetracycline.The concentration dependence of the inhibition reveals that the association constant for the TET repressoretetracycline complex exceeds the one for the TET repressor TET operator complex.The thermal stability of the TET repressor TET operator complex extends up to 60 "C and drops sharply between 63 "C and 70 "C.The TET repressor-TET operator complex is stable be-