gebhart/patrepeval huggingface dataset:
Rapid expansion of the physical and genetic map of the chromosome of Clostridium perfringens CPN50 (1995)

The physical map of the 3.6-megabase chromosome of Clostridium perfringens CPN50 was extended by positioning sites for the endonucleases SfiI and I-CeuI, and in parallel, the gene map was expanded by using a genome scanning strategy. This involved the cloning and sequencing of random chromosomal fragments, identification of the functions of the putative genes by database searches, and then hybridization analysis. The current gene map comprises almost 100 markers, many of which encode housekeeping functions while others are involved in sporulation or pathogenesis. Strikingly, most of the virulence genes were found to be confined to a 1,200-kb segment of the chromosome near oriC, while the pleiotropic regulatory locus, virRS, was situated toward the putative replication terminus. A comparison of the gene maps of three endospore-forming bacilli, C. perfringens, Clostridium beijerinckii, and Bacillus subtilis, revealed a similar order and distribution of key sporulation and heat shock genes which might reflect an ancient evolutionary relationship.
Expression and regulation of a proenkephalin beta-galactosidase fusion gene in the reproductive system of transgenic mice. (1992)

A fusion gene containing 3 kilobases of human proenkephalin 5'-flanking sequences and 1 kilobase of human proenkephalin 3'-flanking sequence and the easily visualized histochemical marker, Escherichia coli beta-galactosidase, was used to study the function of cis-regulatory elements within the human proenkephalin gene in transgenic mice. Here data are presented on expression and regulation of this fusion gene in the reproductive system of three independent lines of transgenic mice. Within the male reproductive system, the fusion gene is expressed in the proximal epididymis and in developing germinal cells but not in mature or elongating spermatids. In the female reproductive system, the transgene was expressed at low basal levels, but expression was dramatically stimulated in the ovary and oviduct by hormonal stimulation and pregnancy; additionally, expression was induced at the uteroplacental junction in pregnant mice. Taken together these observations suggest that critical sequences for expression and regulation of the proenkephalin gene within the reproductive system are contained within sequences of the construct.
Synthesis of optically active amino acids from alpha-keto acids with Escherichia coli cells expressing heterologous genes (1997)

We describe a simple method for enzymatic synthesis of L and D amino acids from alpha-keto acids with Escherichia coli cells which express heterologous genes. L-amino acids were produced with thermostable L-amino acid dehydrogenase and formate dehydrogenase (FDH) from alpha-keto acids and ammonium formate with only an intracellular pool of NAD+ for the regeneration of NADH. We constructed plasmids containing, in addition to the FDH gene, the genes for amino acid dehydrogenases, including i.e., leucine dehydrogenase, alanine dehydrogenase, and phenylalanine dehydrogenase. L-Leucine, L-valine, L-norvaline, L-methionine, L-phenylalanine, and L-tyrosine were synthesized with the recombinant E. coli cells with high chemical yields (> 80%) and high optical yields (up to 100% enantiomeric excess). Stereospecific conversion of various alpha-keto acids to D amino acids was also examined with recombinant E. coli cells containing a plasmid coding for the four heterologous genes of the thermostable enzymes D-amino acid aminotransferase, alanine racemase, L-alanine dehydrogenase, and FDH. Optically pure D enantiomers of glutamate and leucine were obtained.
Vir Proteins Stabilize VirB5 and Mediate Its Association with the T Pilus of Agrobacterium tumefaciens (1999)

Three VirB proteins (VirB1*, VirB2, and VirB5) have been implicated as putative components of the T pilus from Agrobacterium tumefaciens, which likely mediates binding to plant cells followed by transfer of genetic material. Recently, VirB2 was indeed shown to be its major component (E.-M. Lai and C. I. Kado, J. Bacteriol. 180:2711-2717, 1998). Here, the influence of other Vir proteins on the stability and cellular localization of VirB1*, VirB2, and VirB5 was analyzed. Solubility of VirB1* and membrane association of VirB2 proved to be inherent features of these proteins, independent of virulence gene induction. In contrast, cellular levels of VirB5 were strongly reduced in the absence of other Vir proteins, indicating its stabilization by protein-protein interactions. The assembly and composition of the T pilus were analyzed in nopaline strain C58(pTiC58), its flagellum-free derivative NT1REB(pJK270), and octopine strain A348(pTiA6) following optimized virulence gene induction on solid agar medium. In all strains VirB2 was the major pilus component and VirB5 cofractionated during several purification steps, such as ultracentrifugation, gel filtration, and sucrose gradient centrifugation. VirB5 may therefore be directly involved in pilus assembly, possibly as minor component. In contrast, secreted VirB1* showed no association with the T pilus. In-frame deletions in genes virB1, virB2, virB5, and virB6 blocked the formation of virulence gene-dependent extracellular high-molecular-weight structures. Thus, an intact VirB machinery as well as VirB2 and VirB5 are required for T-pilus formation.
Dual-mode temperature compensation technique for laser stabilization to a crystalline whispering gallery mode resonator (2012)

Frequency stabilization of a diode laser locked to a whispering gallery mode (WGM) reference resonator made of a MgF<sub>2</sub> single crystal is demonstrated. The strong thermal dependence of the difference frequency between two orthogonally polarized TE an TM modes (dual-mode frequency) of the optically anisotropic crystal material allows sensitive measurement of the resonator's temperature within the optical mode volume. This dual-mode signal was used as feedback for self-referenced temperature stabilization to nanokelvin precision, resulting in frequency stability of 0.3 MHz/h at 972 nm, which was measured by comparing with an independent ultrastable laser.
Retinal effects of ultrashort laser pulses in the rabbit eye. (1995)

The low energies required for visible lesion production in live rabbit eyes raise new questions surrounding ultrashort pulse propagation in ocular media, energy deposition at the retina, and mechanisms limiting retinal damage from ultrashort laser pulses.
Operation of multi-finger graphene quantum capacitance varactors using planarized local bottom gate electrodes (2012)

The operation of multi-finger graphene quantum capacitance varactors fabricated using a planarized local bottom gate electrode, HfO2 gate dielectric, and large-area graphene is described. As a function of the gate bias, the devices show a room-temperature capacitance tuning range of 1.22–1 over a voltage range of ±2 V. An excellent theoretical fit of the temperature-dependent capacitance-voltage characteristics is obtained when random potential fluctuations with standard deviation of 65 mV are included. The results represent a first step in realizing graphene quantum capacitance varactors for wireless sensing applications.
Integrity assurance in resource-bounded systems through stochastic message authentication (2015)

Assuring communication integrity is a central problem in security. However, overhead costs associated with cryptographic primitives used towards this end introduce significant practical implementation challenges for resource-bounded systems, such as cyber-physical systems. For example, many control systems are built on legacy components which are computationally limited but have strict timing constraints. If integrity protection is a binary decision, it may simply be infeasible to introduce into such systems; without it, however, an adversary can forge malicious messages, which can cause significant physical or financial harm. We propose a formal game-theoretic framework for optimal stochastic message authentication, providing provable integrity guarantees for resource-bounded systems based on an existing MAC scheme. We use our framework to investigate attacker deterrence, as well as optimal design of stochastic message authentication schemes when deterrence is impossible. Finally, we provide experimental results on the computational performance of our framework in practice.
Bicarbonate Resensitization of Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics (2019)

Endovascular infections caused by methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) are a major health care concern, especially infective endocarditis (IE). Standard antimicrobial susceptibility testing (AST) defines most MRSA strains as "resistant" to β-lactams, often leading to the use of costly and/or toxic treatment regimens. In this investigation, five prototype MRSA strains, representing the range of genotypes in current clinical circulation, were studied. We identified two distinct MRSA phenotypes upon AST using standard media, with or without sodium bicarbonate (NaHCO<sub>3</sub>) supplementation: one highly susceptible to the antistaphylococcal β-lactams oxacillin and cefazolin (NaHCO<sub>3</sub> responsive) and one resistant to such agents (NaHCO<sub>3</sub> nonresponsive). These phenotypes accurately predicted clearance profiles of MRSA from target tissues in experimental MRSA IE treated with each β-lactam. Mechanistically, NaHCO<sub>3</sub> reduced the expression of two key genes involved in the MRSA phenotype, <i>mecA</i> and <i>sarA</i>, leading to decreased production of penicillin-binding protein 2a (that mediates methicillin resistance), in NaHCO<sub>3</sub>-responsive (but not in NaHCO<sub>3</sub>-nonresponsive) strains. Moreover, both cefazolin and oxacillin synergistically killed NaHCO<sub>3</sub>-responsive strains in the presence of the host defense antimicrobial peptide (LL-37) in NaHCO<sub>3</sub>-supplemented media. These findings suggest that AST of MRSA strains in NaHCO<sub>3</sub>-containing media may potentially identify infections caused by NaHCO<sub>3</sub>-responsive strains that are appropriate for β-lactam therapy.
Probing of C‐terminal lysine variation in a recombinant monoclonal antibody production using Chinese hamster ovary cells with chemically defined media (2012)

C-terminal lysine (C-K) variants are commonly observed in therapeutic monoclonal antibodies and recombinant proteins. Heterogeneity of C-K residues is believed to result from varying degree of proteolysis by endogenous carboxypeptidase(s) during cell culture production. The achievement of batch-to-batch culture performance and product quality reproducibility is a key cell culture development criterion. Understanding the operational parameters affecting C-K levels provides valuable insight into the cell culture process. A CHO cell line X expressing a recombinant antibody was selected as the model cell line due to the exhibited sensitivity of its C-K level to the process conditions. A weak cation exchange chromatography (WCX) method with or without carboxypeptidase B (CpB) treatment was developed to monitor the C-K level for in-process samples. The effects of operating conditions (i.e., temperature and culture duration) and media trace elements (copper and zinc) on C-K variants were studied. The dominant effect on C-K level was identified as the trace elements concentration. Specifically, increased C-K levels were observed with increase of copper concentration and decrease of zinc concentration in chemically defined medium. Further, a hypothesis for C-K processing with intracellular and extracellular carboxypeptidase activity was proposed, based on preliminary intracellular carboxypeptidase Western blot results and the extracellular HCCF holding study.
Condensed Heteroaromatic Ring Systems. XXII. Simple and General Synthesis of 1H-Pyrrolopyridines (1992)

Four kinds of 1 H-pyrrolopyridines having no substituent were simply and easily synthesized by the palladium-catalyzed reaction of easily available nitropyridine derivatives with (Z)-1 -ethoxy-2-tributylstannylethene as a key reaction
Purification and Characterization of Methylmalonate-semialdehyde Dehydrogenase from Rat Liver (1989)

Methylmalonate semialdehyde dehydrogenase was purified from rat liver in order to define the distal portion of valine catabolism and related pathways in mammals. The purified enzyme is active with malonate semialdehyde and consumes both stereoisomers of methylmalonate semialdehyde, implicating a single semialdehyde dehydrogenase in the catabolism of valine, thymine, and compounds catabolized by way of beta-alanine. The oxidation of malonate and methylmalonate semialdehydes by this enzyme is CoA-dependent, the products being acetyl-CoA and propionyl-CoA, respectively. Expected activity with ethylmalonate semialdehyde as substrate was not found. Methylmalonate semialdehyde dehydrogenase was separated on DEAE-Sephacel into two isoforms which differ in mobility during nondenaturing polyacrylamide gel electrophoresis. The two forms are immunologically cross-reactive and exhibit the same N-terminal sequence, suggesting that one form is the product of the other. The monomer molecular mass, determined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, was 58 kDa. The native molecular mass, estimated by gel filtration, was 250 kDa, suggesting a tetrameric structure.
Massive osteoarticular knee allografts: structural changes evaluated with CT. (1995)

CT effectively depicted the structural changes during allograft incorporation and was superior to plain radiography for the detection of insufficiency fractures. The use of CT for follow-up of massive osteoarticular knee allografts provides additional information concerning the readiness of the graft for weight bearing.
Combined image- and world-space tracking in traffic scenes (2017)

Tracking in urban street scenes plays a central role in autonomous systems such as self-driving cars. Most of the current vision-based tracking methods perform tracking in the image domain. Other approaches, e.g. based on LIDAR and radar, track purely in 3D. While some vision-based tracking methods invoke 3D information in parts of their pipeline, and some 3D-based methods utilize image-based information in components of their approach, we propose to use image- and world-space information jointly throughout our method. We present our tracking pipeline as a 3D extension of image-based tracking. From enhancing the detections with 3D measurements to the reported positions of every tracked object, we use world-space 3D information at every stage of processing. We accomplish this by our novel coupled 2D-3D Kalman filter, combined with a conceptually clean and extendable hypothesize-and-select framework. Our approach matches the current state-of-the-art on the official KITTI benchmark, which performs evaluation in the 2D image domain only. Further experiments show significant improvements in 3D localization precision by enabling our coupled 2D-3D tracking.
Application Of The Score Algorithm And Score Extensions To Sorting In The Rank-L Spectral Self-coherence Environment (2005)

The Self Coherence REstoral (SCORE) algorithm has been shown to blindly extract a single signal of interest with spectra correlation at a known value of frequency separation (e.g., baud rate) from an arbitrary number of interferers without correlation at that frequency separation. This paper investigates the ability of the SCORE approach to extract cyclostationary signals from a rank L spectral self-coherence environment where L signals exhibit spectral correlation at the same frequency separation. It is shown analytically and by computer simulation that the SCORE algorithm can separate multiple signals with spectral self-coherence at the same value of frequency separation, provided that those signals have different self-coherence strengths. An extension of the SCORE algorithm is also developed that can separate sig- nals if their complex-valued spectral self-coherence functions are different, e.g., in a communications net where the signals have dif- ferent timing phases. It is shown that the SINR of the separated signals approaches the maximum attainable SINR.
The Polysaccharide Capsule of <i>Campylobacter jejuni</i> Modulates the\nHost Immune Response (2013)

Campylobacter jejuni is a major cause of bacterial diarrheal disease worldwide. The organism is characterized by a diversity of polysaccharide structures, including a polysaccharide capsule. Most C. jejuni capsules are known to be decorated nonstoichiometrically with methyl phosphoramidate (MeOPN). The capsule of C. jejuni 81-176 has been shown to be required for serum resistance, but here we show that an encapsulated mutant lacking the MeOPN modification, an mpnC mutant, was equally as sensitive to serum killing as the nonencapsulated mutant. A nonencapsulated mutant, a kpsM mutant, exhibited significantly reduced colonization compared to that of wild-type 81-176 in a mouse intestinal colonization model, and the mpnC mutant showed an intermediate level of colonization. Both mutants were associated with higher levels of interleukin 17 (IL-17) expression from lamina propria CD4+ cells than from cells from animals infected with 81-176. In addition, reduced levels of Toll-like receptor 4 (TLR4) and TLR2 activation were observed following in vitro stimulation of human reporter cell lines with the kpsM and mpnC mutants compared to those with wild-type 81-176. The data suggest that the capsule polysaccharide of C. jejuni and the MeOPN modification modulate the host immune response.
Recent additions in the treatment of cough. (2014)

Recent additions in the treatment of chronic cough have been significant as they consider cough to have a unifying diagnosis of cough hypersensitivity with or without the presence of a neuropathic basis. Primarily, effective treatments for chronic cough target these areas and include behavioural treatment such as speech pathology and pharmaceutical treatment with neuromodulating medications such as gabapentin.
Calculated dosimetric parameters of the IoGold 125I source model 3631‐A (1998)

Basic dosimetric parameters as recommended by the AAPM Task Group No. 43 (TG-43) have been determined for recently available IoGold 125I brachytherapy seeds. Monte Carlo methods (MCNP) were used in the calculation of these parameters in water, and results compared with soon to be published experimental parameters also for 125I IoGold seeds as well with parameters for model 6702 and 6711 125I seeds. These parameters were the radial dose function, anisotropy factor and constant, and the dose rate constant. Using MCNP, values for the radial dose function at 0.5, 2.0, and 5.0 cm were 1.053, 0.877, and 0.443, respectively. The anisotropy factor was 0.975, 0.946, 0.945, and 0.952 at 0.5, 1.0, 2.0, and 5.0 cm, respectively, with an anisotropy constant of 0.95. The IoGold dose rate constant was determined by excluding the low energy titanium characteristic x rays produced in the IoGold titanium capsule. Using this post TG-43 revised NIST air kerma methodology, the IoGold dose rate constant was 0.96 cGy h-1 U-1. These calculatively determined parameters for IoGold seeds were compared with those determined experimentally for IoGold seeds, and also compared with parameters determined for model 6702 and 6711 seeds as presented in TG-43.
Cloning, expression, and nucleotide sequence of genes involved in production of pediocin PA-1, and bacteriocin from Pediococcus acidilactici PAC1.0 (1992)

The production of pediocin PA-1, a small heat-stable bacteriocin, is associated with the presence of the 9.4-kbp plasmid pSRQ11 in Pediococcus acidilactici PAC1.0. It was shown by subcloning of pSRQ11 in Escherichia coli cloning vectors that pediocin PA-1 is produced and, most probably, secreted by E. coli cells. Deletion analysis showed that a 5.6-kbp SalI-EcoRI fragment derived from pSRQ11 is required for pediocin PA-1 production. Nucleotide sequence analysis of this 5.6-kbp fragment indicated the presence of four clustered open reading frames (pedA, pedB, pedC, and pedD). The pedA gene encodes a 62-amino-acid precursor of pediocin PA-1, as the predicted amino acid residues 19 to 62 correspond entirely to the amino acid sequence of the purified pediocin PA-1. Introduction of a mutation in pedA resulted in a complete loss of pediocin production. The pedB and pedC genes, encoding proteins of 112 and 174 amino acid residues, respectively, are located directly downstream of the pediocin structural gene. Functions could not be assigned to their gene products; mutation analysis showed that the PedB protein is not involved in pediocin PA-1 production. The mutation analysis further revealed that the fourth gene, pedD, specifying a relatively large protein of 724 amino acids, is required for pediocin PA-1 production in E. coli. The predicted pedD protein shows strong similarities to several ATP-dependent transport proteins, including the E. coli hemolysin secretion protein HlyB and the ComA protein, which is required for competence induction for genetic transformation in Streptococcus pneumoniae.(ABSTRACT TRUNCATED AT 250 WORDS)
Mice lacking a transcriptional corepressor Tob are predisposed to cancer (2003)

tob is a member of antiproliferative family genes. Mice lacking tob are prone to spontaneous formation of tumors. The occurrence rate of diethylnitrosamine-induced liver tumors is higher in tob(-/-) mice than in wild-type mice. tob(-/-)p53(-/-) mice show accelerated tumor formation in comparison with single null mice. Expression of cyclin D1 mRNA is increased in the absence of Tob and is reduced by Tob. Tob acts as a transcriptional corepressor and suppresses the cyclin D1 promoter activity through an interaction with histone deacetylase. Levels of tob mRNA are often decreased in human cancers, implicating tob in cancer development.
Childhood and adolescent cancer statistics, 2014 (2014)

In this article, the American Cancer Society provides estimates of the number of new cancer cases and deaths for children and adolescents in the United States and summarizes the most recent and comprehensive data on cancer incidence, mortality, and survival from the National Cancer Institute, the Centers for Disease Control and Prevention, and the North American Association of Central Cancer Registries (which are reported in detail for the first time here and include high-quality data from 45 states and the District of Columbia, covering 90% of the US population). In 2014, an estimated 15,780 new cases of cancer will be diagnosed and 1960 deaths from cancer will occur among children and adolescents aged birth to 19 years. The annual incidence rate of cancer in children and adolescents is 186.6 per 1 million children aged birth to 19 years. Approximately 1 in 285 children will be diagnosed with cancer before age 20 years, and approximately 1 in 530 young adults between the ages of 20 and 39 years is a childhood cancer survivor. It is therefore likely that most pediatric and primary care practices will be involved in the diagnosis, treatment, and follow-up of young patients and survivors. In addition to cancer statistics, this article will provide an overview of risk factors, symptoms, treatment, and long-term and late effects for common pediatric cancers.