gebhart/patrepeval huggingface dataset:
Effects of Sarcocystosis on Milk Production of Dairy Cows (1983)

Sixteen multiparous Holstein cows were allotted randomly to four groups of four cows each. Cows in 1 and 2 were uninfected. Those in 3 received 60,000 and those in 4 received 120,000 Sarcocystis bovicanis sporocysts per os approximately 30 days before the expected onset of lactation to produce nonclinical and clinical infections in 3 and 4, respectively. Combined stresses of infection, parturition, lactation, and high ambient temperatures caused all infected cows to develop clinical illness. Clinical signs included fever, anemia, glossitis, myositis, nasal discharge, hypersalivation, anorexia, and hind limb weakness; two cows died and two others were killed in extremis. Six cows in 3 and 4 developed high Sarcocystis-specific immunoglobulin G1 antibody. Uninfected control cows had no clinical signs and no rising concentrations of antibody against Sarcocystis antigen. When lactation began, cows were milked twice daily, and milk production was recorded for 70 consecutive days. All sarcocystis-infected cows (3 and 4) decreased feed intake and milk production compared with uninfected controls. The Wisconsin Mastitis Test on milk production compared with uninfected controls. The Wisconsin Mastitis Test on milk samples at 1, 2, 4, 8, and 12 wk of lactation did not differ among groups.
Synthesizing Biomolecule-Based Boolean Logic Gates (2012)

One fascinating recent avenue of study in the field of synthetic biology is the creation of biomolecule-based computers. The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices. Boolean logic gates are at the core of the operational machinery of these parts, and hence to make biocomputers a reality, biomolecular logic gates become a necessity. Indeed, with the advent of more sophisticated biological tools, both nucleic acid- and protein-based logic systems have been generated. These devices function in the context of either test tubes or living cells and yield highly specific outputs given a set of inputs. In this review, we discuss various types of biomolecular logic gates that have been synthesized, with particular emphasis on recent developments that promise increased complexity of logic gate circuitry, improved computational speed, and potential clinical applications.
Tumour necrosis factor-α induces superoxide anion generation in mitochondria of L929 cells (1993)

Within a few minutes after addition to L929 cells, tumour necrosis factor-alpha (TNF alpha) induced an increase in lucigenin-enhanced chemiluminescence that could be inhibited by superoxide dismutase. The generation of superoxide anion (O2.-) was sensitive to treatment with rotenone, antimycin A and cyanide, indicating that the signal originated from mitochondria. The mechanism of production of O2.- was shown to be independent of ATP synthesis, as uncoupling of this event from mitochondrial electron transport did not alter the generation of O2.- induced by TNF alpha. Chemiluminescence was further dependent on the presence of extracellular calcium, suggesting a role for this cation as a second messenger. This hypothesis was supported by the finding that inhibition of mitochondrial calcium uptake by Ruthenium Red exerted a protective effect on TNF alpha-treated L929 cells. Increased O2.- generation was followed by a marked decrease in mitochondrial dehydrogenase activity and cellular ATP levels, while cell membrane permeability was moderately increased. A role for mitochondrial O2.- generation in TNF alpha cytotoxicity was further supported by the finding that resistant L929 cells had decreased ability to produce O2.- in response to TNF alpha. In addition, we detected a decreased activity of the mitochondrial enzyme succinate dehydrogenase in these cells, suggesting that this component of the respiratory chain might be an important contributor to the TNF alpha-induced generation of O2.-.
Suppression of basic fibroblast growth factor‐induced angiogenesis by a specific chymase inhibitor, BCEAB, through the chymase‐angiotensin‐dependent pathway in hamster sponge granulomas (2002)

1. We investigated the profound involvement of mast cell chymase, an alternative angiotensin II-generating enzyme, in angiogenesis using a specific chymase inhibitor. We also studied the functional profiles of this novel inhibitor in basic fibroblast growth factor (bFGF)-induced angiogenesis. 2. In this study, angiogenesis was induced by daily injections of bFGF (0.3 micro g site(-1) day(-1)), angiotensin I (2 nmol site(-1) day(-1)) or angiotensin II (2 nmol site(-1) day(-1)) into sponges implanted to male hamsters subcutaneously for 7 days. Angiogenesis in the granulation tissue surrounding sponges was evaluated by measuring the haemoglobin (Hb) content and local blood flow as the parameters for angiogenesis. 3. A chymase inhibitor, BCEAB (4-[1-[[bis-(4-methyl-phenyl)-methyl]-carbamoyl]-3-(2-ethoxy-benzyl)-4-oxo-azetidine-2-yloxy]-benzoic acid), was simultaneously administered into the implanted sponges (2 or 5 nmol site(-1) day(-1), for 7 days) treated with bFGF and strongly suppressed the haemoglobin contents in sponge granulomas. In the studies using a laser doppler perfusion imager, BCEAB (5 nmol site(-1) day(-1)) also attenuated the bFGF-induced increase of local blood flow around the implanted sponge granuloma. 4. In bFGF-induced angiogenesis, chymase activity in sponge granulomas was substantially increased. It was also confirmed that the chymase activity increased by bFGF was significantly and dose-dependently inhibited by BCEAB (2, 5 nmol site(-1) day(-1)). 5. BCEAB inhibited the Hb contents and the expression of vascular endothelial growth factor (VEGF) mRNA induced by angiotensin I but not by angiotensin II. 6. These results suggest that the significance of chymase in bFGF-induced angiogenesis was confirmed, and a novel inhibitor, BCEAB, strongly suppresses the bFGF-induced angiogenesis through the chymase-angiotensin II-VEGF dependent pathway.
Nickel Catalyst Stability toward Carboxylic Acids (2008)

Reduced (unsulfided) nickel catalysts can be used for hydroprocessing sulfur-free Fischer−Tropsch derived feed materials, but catalyst deactivation by metal leaching can be a problem in the presence of carboxylic acids. Leaching of reduced nickel catalysts by carboxylic acids takes place by the formation of nickel carboxylates. Carboxylic acid leaching of nickel can be prevented by operating above the carboxylate decomposition temperature, which was found to be in the range 280−305 °C for the C2−C5 nickel carboxylates. Unfortunately this is not industrially practical, because of the hydrogenolysis propensity of reduced nickel catalysts at these conditions. It was also found that nickel leaching did not monotonically increase with temperature, but was inhibited at >200 °C, probably due to polymerization of the nickel carboxylates.
The cytokine-cosmc signaling axis upregulates the tumor-associated carbohydrate antigen Tn (2016)

Tn antigen (GalNAc-α-O-Ser/Thr), a mucin-type O-linked glycan, is a well-established cell surface marker for tumors and its elevated levels have been correlated with cancer progression and prognosis. There are also reports that Tn is elevated in inflammatory tissues. However, the molecular mechanism for its elevated levels in cancer and inflammation is unclear. In the current studies, we have explored the possibility that cytokines may be one of the common regulatory molecules for elevated Tn levels in both cancer and inflammation. We showed that the Tn level is elevated by the conditioned media of HrasG12V-transformed-BEAS-2B cells. Similarly, the conditioned media obtained from LPS-stimulated monocytes also elevated Tn levels in primary human gingival fibroblasts, suggesting the involvement of cytokines and/or other soluble factors. Indeed, purified inflammatory cytokines such as TNF-α and IL-6 up-regulated Tn levels in gingival fibroblasts. Furthermore, TNF-α was shown to down-regulate the COSMC gene as evidenced by reduced levels of the COSMC mRNA and protein, as well as hypermethylation of the CpG islands of the COSMC gene promoter. Since Cosmc, a chaperone for T-synthase, is known to negatively regulate Tn levels, our results suggest elevated Tn levels in cancer and inflammation may be commonly regulated by the cytokine-Cosmc signaling axis.
Digital Displacement Transducer Using Antiferroelectrics (1985)

Anomalous strain changes are associated with the electric field induced phase transition from an antiferroelectric phase to a ferroelectric one. PZT family ceramics Pb 0.99 Nb 0.02 [(Zr 0.6 Sn 0.4 ) 1- y ,Ti y l 0.98 O 3 are investigated here, revealing digitalized strains or a shape memory effect. These phenomena are explainable in terms of a dielectric phase diagram. Applications are proposed for generating swing motion with a constant amplitude or mechanical clamping at the position with a narrow space.
Impact of multipath channel parameters on channel estimation performance in OFDM systems (2009)

Performance of wireless OFDM systems significantly depends on channel estimation accuracy. However, it is difficult to take into account all possible scenarios as the variance of error at the output of the minimum mean square error (MMSE) estimator depends on the second-order channel statistics. In this paper, we derive the lower and the upper MSE bounds, characterising the best and the worst-case channel estimation performance, and discuss channel conditions when these bounds are attained.
HIV-1 vaccination by needle-free oral injection induces strong mucosal immunity and protects against SHIV challenge (2019)

The oral mucosa is an attractive site for mucosal vaccination, however the thick squamous epithelium limits antigen uptake. Here we utilize a modified needle-free injector to deliver immunizations to the sublingual and buccal (SL/B) tissue of rhesus macaques. Needle-free SL/B vaccination with modified vaccinia Ankara (MVA) and a recombinant trimeric gp120 protein generates strong vaccine-specific IgG responses in serum as well as vaginal, rectal and salivary secretions. Vaccine-induced IgG responses show a remarkable breadth against gp70-V1V2 sequences from multiple clades of HIV-1. In contrast, topical SL/B immunizations generates minimal IgG responses. Following six intrarectal pathogenic SHIV-SF162P3 challenges, needle-free but not topical immunization results in a significant delay of acquisition of infection. Delay of infection correlates with non-neutralizing antibody effector function, Env-specific CD4<sup>+</sup> T-cell responses, and gp120 V2 loop specific antibodies. These results demonstrate needle-free MVA/gp120 oral vaccination as a practical and effective route to induce protective immunity against HIV-1.
Cantharidin‐Based Small Molecules as Potential Therapeutic Agents (2013)

Chemical and pharmacological information on cantharidin-based small molecules was analyzed. The review summarizes new facts about blister beetles' metabolites for the period 2006-2012. General synthetic approaches to cantharidin-based small molecules as well as their chemical transformations and biological activities related to cantharidin, norcantharidin, cantharidimide, and norcantharimide analogs, especially their inhibitory activity of phosphoprotein phosphatases in cancer treatment, were discussed in this mini review, which could help to design new small molecule modulators for other biological models.
The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules (2008)

CysR acts as the functional analogue of the unrelated LysR-type regulator CysB from Escherichia coli, controlling sulphide production in response to acceptor availability. In both bacteria, gene duplication events seem to have taken place which resulted in the evolution of dedicated regulators for the control of sulphonate utilisation. The striking convergent evolution of network topology indicates the strong selective pressure to control the metabolism of the essential but often toxic sulphur-containing (bio-)molecules.
Corrosion Characteristics of Mild Steel in Urea Ammonium Nitrate Fertilizer Solutions (2002)

Anodic polarization studies have been conducted on mild steel in urea ammonium nitrate (UAN) fertilizer solutions comprising 31 wt% urea ([NH2]2CO), 39 wt% ammonium nitrate (NH4NO3), and 30 wt% H2O, with a total N content of 28 wt% (UAN 28-0-0). It was determined that mild steel can spontaneously exhibit either active-passive or passive behavior when immersed in UAN solutions. At 23°C, specimens exhibiting active-passive behavior experienced corrosion rates of ~2 mm/y for pH values in the range of 3 to 8.5. At pH values &lt;3, the corrosion rate increased rapidly, reaching a value of 92 mm/y at a pH of 1.1. Specimens exhibiting passive behavior experienced corrosion rates of ~0.002 mm/y for the pH range of 6 to 8.5. An increase in temperature from 23°C to 60°C increased the corrosion rate of specimens exhibiting active-passive behavior from ~2 mm/y to ~15 mm/y. To minimize corrosion, mild steel storage tanks for liquid UAN fertilizer should be kept free of sludges and other contaminants, which could provide stagnant areas where low pH areas can develop. Further, storage tanks should be painted a light color since darkly painted tanks experience higher temperatures and thus higher corrosion rates.
T-cell protein tyrosine phosphatase deletion results in progressive systemic inflammatory disease (2004)

The deregulation of the immune response is a critical component in inflammatory disease. Recent in vitro data show that T-cell protein tyrosine phosphatase (TC-PTP) is a negative regulator of cytokine signaling. Furthermore, tc-ptp(-/-) mice display immune defects and die within 5 weeks of birth. We report here that tc-ptp(-/-) mice develop progressive systemic inflammatory disease as shown by chronic myocarditis, gastritis, nephritis, and sialadenitis as well as elevated serum interferon-gamma. The widespread mononuclear cellular infiltrates correlate with exaggerated interferon-gamma, tumor necrosis factor-alpha, interleukin-12, and nitric oxide production in vivo. Macrophages grown from tc-ptp(-/-) mice are inherently hypersensitive to lipopolysaccharide, which can also be detected in vivo as an increased susceptibility to endotoxic shock. These results identify T-cell protein tyrosine phosphatase as a key modulator of inflammatory signals and macrophage function.
The AidB Component of the <i>Escherichia coli</i> Adaptive Response to Alkylating Agents Is a Flavin-Containing, DNA-Binding Protein (2005)

Upon exposure to alkylating agents, Escherichia coli increases expression of aidB along with three genes (ada, alkA, and alkB) that encode DNA repair proteins. In order to begin to identify the role of AidB in the cell, the protein was purified to homogeneity, shown to possess stoichiometric amounts of flavin adenine dinucleotide (FAD), and confirmed to have low levels of isovaleryl-coenzyme A (CoA) dehydrogenase activity. A homology model of an AidB homodimer was constructed based on the structure of a four-domain acyl-CoA oxidase. The predicted structure revealed a positively charged groove connecting the two active sites and a second canyon of positive charges in the C-terminal domain, both of which could potentially bind DNA. Three approaches were used to confirm that AidB binds to double-stranded DNA. On the basis of its ability to bind DNA and its possession of a redox-active flavin, AidB is predicted to catalyze the direct repair of alkylated DNA.
Biocompatible polymer brushes grown from model quartz fibres: synthesis, characterisation and in situ determination of frictional coefficient (2010)

Poly(2-(methacryloyloxy)ethyl phosphorylcholine) (PMPC) chains were grown from near-monodisperse 13 µm diameter quartz fibres using surface-initiated atom transfer radical polymerisation (ATRP) at ambient temperature in 1 : 1 methanol–water at 20 °C. A covalently-bound siloxane-based ATRP initiator provided a sufficiently high grafting density to obtain polymer brushes from this model substrate. X-Ray photoelectron spectroscopy indicates that the PMPC brush coverage on this model fibre substrate is both thick and uniform, since the Si signals due to the underlying quartz are obscured. Thermogravimetric analysis (TGA) on selected PMPC-coated quartz fibres indicates a monotonic increase in PMPC brush thickness and reasonably good agreement was obtained with ellipsometry data, which was obtained indirectly for the corresponding PMPC brushes grown in situ from planar silicon wafers placed in the same reaction vessel as the quartz fibres. The dimensions of the thickest PMPC brush grown from the fibres could also be estimated by scanning electron microscopy. FT-IR spectroscopy confirmed a linear increase in the ester carbonyl band intensity for increasing target brush thickness, as expected. Rutherford back-scattering spectrometry (RBS) analyses also reported brush thicknesses that correlated linearly with this ester carbonyl band, but this technique appears to underestimate brush dimensions relative to TGA and ellipsometry. This is presumably due to in situ beam damage during RBS analysis. Friction force microscopy studies were conducted for both PMPC-coated and bare fibres immersed in water. Compared to the bare fibres, the presence of the PMPC chains led to a reduction in the relative frictional coefficient by more than an order of magnitude. A smaller, but still significant, reduction in the friction coefficient was also obtained using ethanol instead of water. This suggests possible applications for PMPC brushes in the context of aqueous lubrication.
Health Economic Benefits and Quality of Life During Improved Glycemic Control in Patients With Type 2 Diabetes Mellitus (1998)

Improved glycemic control of type 2 DM is associated with substantial short-term symptomatic, QOL, and health economic benefits.
Aminohaloborane in Organic Synthesis. IV.<sup>1</sup>A Directed Aldol Condensation Using Vinylaminodichloroborane (1979)

Abstract Continuing our studies on the specific ortho substitution reaction of anilines,2 we tried to extend this methodology to directed aldol condensation3. Namely, N-cyclohexylidencyclohexylamine 1 was treated with boron trichloride and triethylamine in dichloromethane giving N-cyclohexyl-N-1-cyclohexenylaminodi-chloroborane 2, to our knowledge, a new type of aminohaloborane. Similar treatment of N-2-butyliden-cyclohexylamine 3 gave N-cyclohexyl-N-2-butenylamino-dichloroborane (a mixture of E and Z isomers) 4. The physical data satisfied the assigned structures.
A ratio-independent algorithmic analog-to-digital conversion technique (1984)

An algorithmic analog-to-digital conversion technique is described which is capable of achieving high-resolution conversion without the use of matched capacitors in an MOS technology. The exact integral multiplication of the signal required by the conversion is realized through an algorithmic circuit method which involves charge summing with an MOS integrator and exchange of capacitors. A first-order cancellation of the charge injection effect from MOS transistor switches is attained with a combination of differential circuit implementation and an optimum timing scheme. An experimental prototype has been fabricated with a standard 5-/spl mu/m n-well CMOS process. It achieves 12-bit resolution at a sampling rate of 8 kHz. The analog chip area measures 2400 mils/SUP 2/.
Current Concepts and Advances in Graft-Versus-Host Disease Immunology (2021)

Worldwide, each year over 30,000 patients undergo an allogeneic hema-topoietic stem cell transplantation with the intent to cure high-risk hematologic malignancy, immunodeficiency, metabolic disease, or a life-threatening bone marrow failure syndrome. Despite substantial advances in donor selection and conditioning regimens and greater availability of allograft sources, transplant recipients still endure the morbidity and mortality of graft-versus-host disease (GVHD). Herein, we identify key aspects of acute and chronic GVHD pathophysiology, including host/donor cell effectors, gut dysbiosis, immune system and cytokine imbalance, and the interface between inflammation and tissue fibrosis. In particular, we also summarize the translational application of this heightened understanding of immune dysregulation in the design of novel therapies to prevent and treat GVHD.
Rescue of the Skeletal Phenotype of Vitamin D Receptor-Ablated Mice in the Setting of Normal Mineral Ion Homeostasis: Formal Histomorphometric and Biomechanical Analyses (1999)

1,25-Dihydroxyvitamin D3 has been shown to play an important role in vitro in regulating osteoblast gene transcription and promoting osteoclast differentiation. To address the role of the vitamin D receptor (VDR) in skeletal homeostasis, formal histomorphometric analyses were performed in VDR null mice in the setting of impaired mineral ion homeostasis as well as in VDR null mice in whom normal mineral ion homeostasis had been preserved. In hypocalcemic VDR null mice, there was an increase in bone volume as a result of a dramatic increase in osteoid. There was also an increase in the number of osteoblasts without a significant change in the number of osteoclasts. Examination of the growth plate revealed marked disorganization, with an increase in vascularity and matrix. Biomechanical parameters demonstrated increased bone fragility in the hypocalcemic VDR null mice. In the VDR ablated mice in whom normal mineral ion homeostasis had been preserved, none of these measurements was significantly different from those in wild-type littermates raised under identical conditions. Notably, the morphology and width of the growth plate were indistinguishable from those in wild-type controls, demonstrating that a calcium/phosphorus/lactose-enriched diet started at 16 days of age in the VDR null mice permits the development of both normal morphology in the growth cartilage and adjacent metaphysis and normal biomechanical competence of cortical bone. Thus, the principle action of the VDR in skeletal growth, maturation, and remodeling is its role in intestinal calcium absorption. The skeletal consequences of VDR ablation are a result of impaired intestinal calcium absorption and/or the resultant secondary hyperparathyroidism and hypophosphatemia.
Practical Exploit Generation for Intent Message Vulnerabilities in Android (2015)

Android's Inter-Component Communication (ICC) mechanism strongly relies on Intent messages. Unfortunately, due to the lack of message origin verification in Intents, application security completely relies on the programmer's skill and attention. In this paper, we advance the state of the art by developing a method to automatically detect potential vulnerabilities and, most importantly, demonstrate whether they can be exploited or not. To this end, we adopt a formal approach to automatically produce malicious payloads that can trigger dangerous behavior in vulnerable applications. We test our methods on a representative sample of applications, and we find that 29 out of 64 tested applications are potentially vulnerable, while 26 of them are automatically proven to be exploitable.