gebhart/patrepeval huggingface dataset:
Enhanced Survivability of Cloned Calves Derived from Roscovitine-Treated Adult Somatic Cells (2002)

Nuclear transfer to produce cattle is inefficient because 1) donor cells are not easily synchronized in the proper phase of the cell cycle, 2) the nucleus of these cells is not effectively reprogrammed, 3) the rate of attrition of late-term pregnancies is high, and 4) the health of early postnatal calves is compromised. The cyclin dependent kinase 2 inhibitor, roscovitine, was used to maximize cell cycle synchrony and to produce cells that responded more reliably to nuclear reprogramming. Roscovitine-treated adult bovine granulosa cells (82.4%) were more efficiently synchronized (P < 0.05) in the quiescent G0/G1 phase of the cell cycle than were serum-starved cells (76.7%). Although blastocyst development following nuclear transfer was elevated (P < 0.05) in the serum-starved group (21.1%) relative to the roscovitine-treated cells (11.8%), the number of cells in the blastocysts derived from roscovitine-treated cells was higher (P < 0.05) than those derived from the serum-starved group (roscovitine-treated group: 142.8 +/- 6.0 cells; serum-starved group: 86.8 +/- 14.5 cells). The resulting fetal and calf survival after embryo transfer was enhanced in the roscovitine-treated group (seven surviving calves from six pregnancies) compared with serum-starved controls (two calves born, one surviving beyond 60 days, from five pregnancies). Roscovitine culture can predictably synchronize the donor cell cycle and increase the nuclear reprogramming capacity of the cells, resulting in enhanced fetal and calf survival and increased cloning efficiency.
A comparative evaluation of two algorithms for Windows Registry Anomaly Detection (2005)

We present a component anomaly detector for a host-based intrusion detection system (IDS) for Microsoft Windows. The core of the detector is a learning-based anomaly detection algorithm that detects attacks on a host machine by looking for anomalous
Functional Reconstitution of the Purified Mannose Phosphotransferase System of Escherichia coli into Phospholipid Vesicles (1995)

The mannose transporter complex acts by a mechanism which couples translocation with phosphorylation of the substrate. It consists of a hydrophilic subunit (IIABMan) and two transmembrane subunits (IICMan, IIDMan). The purified complex was reconstituted into phospholipid vesicles by octyl glucoside dilution. Glucose export was measured with proteoliposomes which were loaded with radiolabeled glucose and to which purified IIABMan, cytoplasmic phosphorylcarrier proteins, and P-enolpyruvate were added from the outside. Vectorial transport was accompanied by stoichiometric phosphorylation of the transported sugar. Glucose added to the outside of the proteoliposomes was also phosphorylated rapidly but did not compete with vectorial export and phosphorylation of internal glucose. Glucose uptake was measured with proteoliposomes which were loaded with the cytoplasmic phosphoryl carrier proteins and P-enolpyruvate and to which glucose was added from the outside. Vectorial import and phosphorylation occurred with a higher specificity (Km 30 +/- 6 microM, kcat 401 +/- 32 pmol of Glc/micrograms of IICDMan/min) than nonvectorial phosphorylation (Km 201 +/- 43 microM, kcat 975 +/- 88 pmol of Glc/micrograms of IICDMan/min). A new plasmid pTSHIC9 for the controlled overexpression of the cytoplasmic phosphoryl carrier proteins, enzyme I, HPr, and IIAGlc, and a simplified procedure for the purification of these proteins are also described.
Human Immunodeficiency Virus Type 1 tat Gene Enhances Human Cytomegalovirus Gene Expression and Viral Replication (1991)

Clonal lines of human rhabdomyosarcoma (RD) cells, constitutively expressing human immunodeficiency virus type 1 (HIV-1) tat gene (RD tat cell lines) showed enhanced expression of human cytomegalovirus (HCMV) immediate-early (IE) and late (L) proteins upon HCMV infection, as compared with control RD cells. One of the RD tat cell lines produced infectious HCMV. The RD-tat cell lines, following transfection with recombinant plasmids containing the full length of the HCMV-IE enhancer/promoter linked to the bacterial chloramphenicol acetyltransferase (CAT) gene, exhibited an increased CAT expression by the tat product. A chronically HIV-1-infected human T-lymphoid cell line, SupT1, superinfected with HCMV, expressed HCMV-IE proteins while the parental SupT1 cells infected with HCMV were negative. Parental SupT1 cells coinfected with HIV-1 and HCMV also expressed HCMV-IE proteins, indicating that HIV-1-encoded proteins exert a positive regulatory effect on HCMV expression.
Dynamics and Spatial Distribution of β-Lactamase Expression in Pseudomonas aeruginosa Biofilms (2004)

The development of resistance to beta-lactam antibiotics is a problem in the treatment of chronic Pseudomonas aeruginosa infection in the lungs of patients with cystic fibrosis. The main resistance mechanism is high-level expression of the chromosomally encoded AmpC beta-lactamase of P. aeruginosa cells growing in biofilms. Several genes have been shown to influence the level of ampC expression, but little is known about the regulation of ampC expression in P. aeruginosa biofilms. To study the expression of ampC in P. aeruginosa biofilms, we constructed a reporter that consisted of the fusion of the ampC promoter to gfp(ASV) encoding an unstable version of the green fluorescent protein. In vitro biofilms of P. aeruginosa were exposed to the beta-lactam antibiotics imipenem and ceftazidime. Sub-MICs of imipenem significantly induced the monitor system of the biofilm bacteria in the peripheries of the microcolonies, but the centers of the microcolonies remained uninduced. However, the centers of the microcolonies were physiologically active, as shown by experiments with another monitor construction consisting of an arabinose-inducible promoter fused to gfp(ASV). The whole biofilm was induced in the presence of increased imipenem concentrations. Ceftazidime induced the monitor system of the biofilm bacteria as well, but only bacteria in the peripheries of the microcolonies were induced in the presence of even very high concentrations. The experiments illustrate for the first time the dynamic and spatial distributions of beta-lactamase induction in P. aeruginosa cells growing in biofilms. Thus, our experiments show that P. aeruginosa cells growing in biofilms constitute a heterogeneous population unit which may create different antibiotic-selective environments for the bacteria in the biofilm.
Till Death Us Do Part (2001)

T he wonder of multicellular organisms is that each individual cell seems to know what to do, where to be, and how to behave. Such remarkable self-organization relies in part on the surprising alacrity of cells to commit suicide, a process termed apoptosis, should they stray or be misplaced from their normal somatic compartment and so become deprived of the requisite social signals needed for their survival. Nowhere is this phenomenon more evident than in epithelial cells, which derive much of their positional information from their association with their neighbors and with the extracellular matrix. Deprived of such associations, epithelial cells typically undergo detachment-induced apoptosis, or anoikis. Such spontaneous suicide effectively confines epithelial tissues to their correct somatic compartments, ensuring the expeditious deletion of cells misplaced during development or through injury, and potently restraining the emergence of invasive malignancies. Accordingly, inactivation of anoikis is a critical step in the progression of epithelial cancers to an invasive and metastatic form. On page 1829 of this issue, Puthalakath et al. (1) show that detachment of epithelial cells from their extracellular matrix detonates an apoptotic bomb by triggering the release of the pro-apoptotic protein Bmf from the myosin V motor complex of the actin cytoskeleton.
Medical Aspects of Chemical and Biological Warfare (1997)

Abstract : This volume was prepared for military medical educational use. The focus of the information is to foster discussion that may form the basis of doctrine and policy. Until this decade, our military forces had not faced chemical and biological weapons since World War I, and the prevailing attitude has been of sight, out of mind. The Persian Gulf War changed all that. Just the threat that such weapons would be used was itself an effective weapon, as it required us to expend tremendous logistical resources to supply our troops in the desert. Now we know that we must master all relevant aspects of defense against chemical and biological warfare. The Biological Weapons Convention, ratified in 1975, did not slow the massive Soviet program, which continued until early 1992, nor did it prevent the buildup in Iraq between 1985 and 1990. At this time, experts are severely questioning whether verification of compliance with the treaty can be certain. Similar concerns delayed ratification of the Chemical Weapons Convention by the U.S. Senate; nevertheless, the senate ratified the treaty on 24 April 1997. A primary value of the Textbook of Military Medicine series is to preserve the lessons of past wars and, by so doing, demonstrate how current doctrine is built on knowledge that was gained at so high a cost. Medical officers should read this volume, Medical Aspects of Chemical and Biological Warfare, and learn its lessons well. Civilians expect that we in the military will know how to manage chemical and biological casualties. Indeed, if we do not, then who will? The nation expects us to be prepared to defend against all attacks and will be unforgiving of any incapacity on our part.
Beneficial effects of combined colestipol-niacin therapy on coronary atherosclerosis and coronary venous bypass grafts (1987)

The Cholesterol-Lowering Atherosclerosis Study (CLAS) was a randomized, placebo-controlled, angiographic trial testing combined colestipol hydrochloride and niacin therapy in 162 nonsmoking men aged 40 to 59 years with previous coronary bypass surgery. During two years of treatment there was a 26% reduction in total plasma cholesterol, a 43% reduction in low-density lipoprotein cholesterol, plus a simultaneous 37% elevation of high-density lipoprotein cholesterol. This resulted in a significant reduction in the average number of lesions per subject that progressed (<i>P</i>&lt;.03) and the percentage of subjects with new atheroma formation (<i>P</i>&lt;.03) in native coronary arteries. Also, the percentage of subjects with new lesions (<i>P</i>&lt;.04) or any adverse change in bypass grafts (<i>P</i>&lt;.03) was significantly reduced. Deterioration in overall coronary status was significantly less in drug-treated subjects than placebo-treated subjects (<i>P</i>&lt;.001). Atherosclerosis regression, as indicated by perceptible improvement in overall coronary status, occurred in 16.2% of colestipol-niacin treated vs 2.4% placebo treated (<i>P</i>=.002). (<i>JAMA</i>1987;257:3233-3240)
Asymmetric Radio Resource Assignment Scheme for Connection-less Services in CDMA/Shared-TDD Cellular Packet Communications (2005)

The shared time division multiplexing (shared-TDD) scheme has been proposed to accommodate asymmetric communications between uplink and downlink. The accommodation of connection-less services in Shared-TDD systems causes a difficulty of TDD boundary control. This paper proposes a TDD boundary control (resource assignment) scheme, which can optimize a position of the TDD boundary based on the ratio of uplink to downlink traffic in code division multiple access (CDMA)/shared-TDD systems with connection-less services. The proposed scheme controls the TDD boundary based on the estimated uplink and downlink traffic. Computer simulations show that the proposed scheme effectively controls the radio resource, and thus improves total system throughput performance.
Identity of Leu-19 (CD56) leukocyte differentiation antigen and neural cell adhesion molecule. (1989)

Neural cell adhesion molecule (N-CAM) is a membrane glycoprotein expressed on neural and muscle tissues that is involved in homotypic adhesive interactions. We have demonstrated that N-CAM also is expressed on hematopoietic cells, and is recognized by the anti-Leu-19 mAb. Leu-19 is preferentially expressed on NK cells and T lymphocytes that mediate MHC-unrestricted cytotoxicity, but is also present on some myeloid leukemia cell lines. On NK cells, T cells, the KG1a.5 hematopoietic cell line, and a neuroblastoma cell line, Leu-19 is a approximately 140-kD polypeptide with N-linked carbohydrates and abundant sialic acid residues. Sequential immunoprecipitation and peptide mapping demonstrated that the Leu-19 and N-CAM molecules expressed on leukocyte and neuroblastoma cell lines are similar structures. These findings suggest that the Leu-19 antigen on leukocytes may be involved in cell adhesion, analogous to the function on N-CAM on neural cells.
Microbial Genescapes: Phyletic and Functional Patterns of ORF Distribution among Prokaryotes (1998)

We have implemented a statistically based approach to comparative genomics that allows us to define and characterize distributional patterns of conceptually translated open reading frames (ORFs) at different confidence levels based on pairwise FASTA matches. In this report, we apply this methodology to nine microbial genomes, focusing particularly on phyletic and functional patterns of ORF distribution within and between the two prokaryotic domains of life, Bacteria and Archaea. We examine patterns of presence and absence of matches, determine the universal ORF set, analyze features of genome specialization between closely related organisms, and present genomic evidence for the monophyly of Archaea. These analyses illustrate how a quantitative approach to comparative genomics can illuminate questions of fundamental biological significance.
Melatonin site and mechanism of action: Single or multiple? (1997)

By affecting the entrainment pathways of the biologic clock, melatonin has a major influence on the circadian and seasonal organization of vertebrates. In addition, a number of versatile functions that far transcend melatonin actions on photoperiodic time measurement and circadian entrainment have emerged. Melatonin is a free radical scavenger and antioxidant and it has a significant immunomodulatory activity, being presumably a major factor in an organism's defense toxic agents and invading organisms. Besides affecting specific receptors in cell membranes to exert its effects, the interaction of melatonin with nuclear receptor sites and with intracellular proteins, like calmodulin or tubulin-associated proteins, as well as the direct antioxidant effects of melatonin, may explain many general functions of the pineal hormone.
Reversible Inactivation of the Tumor Suppressor PTEN by H2O2 (2002)

The tumor suppressor PTEN regulates cell migration, growth, and survival by removing the 3'-phosphate of phosphoinositides. Exposure of purified PTEN or of cells to H(2)O(2) resulted in inactivation of PTEN in a time- and H(2)O(2) concentration-dependent manner. Analysis of various cysteine mutants, including mass spectrometry of tryptic peptides, indicated that the essential Cys(124) residue in the active site of PTEN specifically forms a disulfide with Cys(71) during oxidation by H(2)O(2). The reduction of H(2)O(2)-oxidized PTEN in cells appears to be mediated predominantly by thioredoxin. Thus, thioredoxin was more efficient than glutaredoxin, glutathione, or a 14-kDa thioredoxin-like protein with regard to the reduction of oxidized PTEN in vitro. Thioredoxin co-immunoprecipitated with PTEN from cell lysates; and incubation of cells with 2,4-dinitro-1-chlorobenzene (an inhibitor of thioredoxin reductase) delayed the reduction of oxidized PTEN, whereas incubation with buthioninesulfoximine (an inhibitor of glutathione biosynthesis) did not. These results suggest that the reversible inactivation of PTEN by H(2)O(2) might be important for the accumulation of 3'-phosphorylated phosphoinositides and that the uncontrolled generation of H(2)O(2) associated with certain pathological conditions might contribute to cell proliferation by inhibiting PTEN function.
Modeling of SOI FET for RF switch applications (2010)

This paper presents the modeling of an SOI FET for RF switch applications. Given that the HF small-signal predictability, i.e. the insertion loss and the isolation, is a common state of the art, the study focuses on the modeling of the non-linearity of the FET. The non-linearity of an SOI FET switch arises from not just the transistor, but also the SOI substrate through various mechanisms. First the non-linearity is caused by the voltage imbalance, a direct result of the substrate loss, in a switch made of many FETs stacked in series. The voltage imbalance is the main non-linearity contributor to a FET switch at high-power levels. Secondly the substrate itself is non-linear and sets the harmonic floor. Besides the substrate, the impact of other important SOI physics, such as the floating-body effect and the parasitic BJT effect, to the switch linearity will also be discussed. Finally a hybrid model that combines PSP as the FET core and a layout-dependent non-linear SOI substrate model is presented, and excellent non-linearity predictability was demonstrated on a real-life RF switch.
Insertion Mutagenesis of Embryonal Carcinoma Cells by Retroviruses (1985)

Mutagenesis was studied in cultured F9 embryonal carcinoma cells infected with a variant of Moloney murine leukemia virus. Proviral insertion induced the inactivation of the hypoxanthine phosphoribosyltransferase locus, and the virus was used to isolate the mutated genes rapidly. Mutagenesis by these methods may be useful for the genetic dissection of the various mammalian cell phenotypes.
Ixodes ticks belonging to the Ixodes ricinus complex encode a family of anticomplement proteins (2007)

The alternative pathway of complement is an important innate defence against pathogens including ticks. This component of the immune system has selected for pathogens that have evolved countermeasures. Recently, a salivary protein able to inhibit the alternative pathway was cloned from the American tick Ixodes scapularis (Valenzuela et al., 2000; J. Biol. Chem. 275, 18717-18723). Here, we isolated two different sequences, similar to Isac, from the transcriptome of I. ricinus salivary glands. Expression of these sequences revealed that they both encode secreted proteins able to inhibit the complement alternative pathway. These proteins, called I. ricinus anticomplement (IRAC) protein I and II, are coexpressed constitutively in I. ricinus salivary glands and are upregulated during blood feeding. Also, we demonstrated that they are the products of different genes and not of alleles of the same locus. Finally, phylogenetic analyses demonstrate that ticks belonging to the Ixodes ricinus complex encode a family of relatively small anticomplement molecules undergoing diversification by positive Darwinian selection.
Deep Iterative and Adaptive Learning for Graph Neural Networks (2019)

In this paper, we propose an end-to-end graph learning framework, namely Deep Iterative and Adaptive Learning for Graph Neural Networks (DIAL-GNN), for jointly learning the graph structure and graph embeddings simultaneously. We first cast the graph structure learning problem as a similarity metric learning problem and leverage an adapted graph regularization for controlling smoothness, connectivity and sparsity of the generated graph. We further propose a novel iterative method for searching for a hidden graph structure that augments the initial graph structure. Our iterative method dynamically stops when the learned graph structure approaches close enough to the optimal graph. Our extensive experiments demonstrate that the proposed DIAL-GNN model can consistently outperform or match state-of-the-art baselines in terms of both downstream task performance and computational time. The proposed approach can cope with both transductive learning and inductive learning.
ChemInform Abstract: Fast Li+ Ion Conduction in Li2O‐Al2O3‐TiO2‐SiO2‐P2O5 Glass‐Ceramics. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Discrimination gain to optimize detection and classification (1997)

A method for managing agile sensors to optimize detection and classification based on discrimination gain is presented. Expected discrimination gain is used to determine threshold settings and search order for a collection of discrete detection cells. This is applied in a low signal-to-noise environment where target-containing cells must be sampled many times before a target can be detected or classified with high confidence. The goal of sensor management is interpreted here to be to direct sensors to optimize the probability densities produced by a data fusion system that they feed. The use of discrimination is motivated by its interpretation as a measure of the relative likelihood for alternative probability densities. This is studied in a problem where a single sensor can be directed at any detection cell in the surveillance volume for each sample. Bayes rule is used to construct a recursive estimator for the cell target probabilities. The expected discrimination gain is predicted for each cell using its current target probability estimates. This gain is used to select the optimal cell for the next sample. The expected discrimination gains can be maintained in a binary search tree structure for computational efficiency. The computational complexity of this algorithm is proportional to the height of the tree which is logarithmic in the number of detection cells. In a test case for a single 0 dB Gaussian target, the error rate for discrimination directed search was similar to the direct search result against a 6 dB target.
<title>Ophthalmic applications of femtosecond lasers</title> (1999)

We investigated three potential femtosecond laser ophthalmic procedures: intrastromal refractive surgery, transcleral photodisruptive glaucoma surgery and photodisruptive ultrasonic lens surgery. A highly reliable, all-solid-state system was used to investigate tissue effects and demonstrate clinical practicality. Compared with longer duration pulses, femtosecond laser-tissue interactions are characterized by smaller and more deterministic photodisruptive energy thresholds, smaller shock wave and cavitation bubble sizes. Scanning a 5 (mu) spot below the target tissue surface produced contiguous tissue effects. Various scanning patterns were used to evaluate the efficacy, safety, and stability of three intrastromal refractive procedures in animal eyes: corneal flap cutting, keratomileusis, and intrastromal vision correction (IVC). Superior dissection and surface quality results were obtained for the lamellar procedures. IVC in rabbits revealed consistent, stable pachymetric changes, without significant inflammation or corneal transparency degradation. Transcleral photodisruption was evaluated as a noninvasive method for creating partial thickness scleral channels to reduce elevated intraocular pressure associated with glaucoma. Photodisruption at the internal scleral surface was demonstrated by focusing through tissue in vitro without collateral damage. Femtosecond photodisruptions nucleated ultrasonically driven cavitation to demonstrate non-invasive destruction of in vitro lens tissue. We conclude that femtosecond lasers may enable practical novel ophthalmic procedures, offering advantages over current techniques.