gebhart/patrepeval huggingface dataset:
Identification and Characterization of a Novel Protein Kinase, TESK1, Specifically Expressed in Testicular Germ Cells (1995)

We have isolated cDNA clones encoding the rat and human forms of a novel protein kinase, termed TESK1 (testis-specific protein kinase 1). Sequence analysis indicates that rat TESK1 contains 628 amino acid residues, composed of an N-terminal protein kinase consensus sequence followed by a C-terminal proline-rich region. Human TESK1 contains 626 amino acids, sharing 92% amino acid identity with its rat counterpart. The protein kinase domain of TESK1 is structurally similar to those of LIMK (LIM motif-containing protein kinase)-1 and LIMK2, with 49-50% sequence identity. Phylogenetic analysis of the protein kinase domains revealed that TESK1 is most closely related to a LIMK subfamily. Chromosomal localization of human TESK1 gene was assigned to 9p13. Anti-TESK1 antibody raised against the C-terminal peptide of TESK1 recognized two polypeptides of 68 and 80 kDa in cell lysates of COS cells transfected with human TESK1 cDNA expression plasmid. TESK1 protein expressed in COS cells exhibited serine/threonine kinase activity, when myelin basic protein was used as a substrate. Northern blot analysis revealed that TESK1 mRNA was specifically expressed in rat and mouse testicular germ cells. The TESK1 mRNA in the testis was detectable only after the 18th day of postnatal development of mice and was mainly expressed in the round spermatids. These observations suggest that TESK1 has a specific function in spermatogenesis.
Mechanism of extraction of chymotrypsin into isooctane at very low concentrations of aerosol OT in the absence of reversed micelles (1994)

Chymotrypsin is easily extracted from an aqueous solution into isooctane containing the anionic surfactant aerosol OT (AOT). The concentration of AOT needed to efficiently extract 0.5 mg/mL CMT is as low as 1 mM and as low as 0.2 mM AOT was sufficient to extract the protein into isooctane. The extraction process was unaffected by 10% (v/v) ethyl acetate in the isooctane phase. Moreover, spectroscopic analysis by electron paramagnetic resonance indicated that CMT did not exist inside a discreet water pool of a reversed micelle. Calculations of the number of AOT molecules associated per extracted CMT molecule indicate that only ca. 30 surfactant molecules interact with the protein, a value too low for reversed micellar incorporation of the protein in isooctane. These studies suggested that reversed micelles do not need to be involved in the actual transfer of the protein from the aqueous to the organic phase and protein solubilization in the organic phase is possible in the absence of reversed micelles. Based on these findings, a new mechanism has been proposed herein for protein extraction via the phase transfer method involving ionic surfactants. The central theme of this mechanism is the formation of an electrostatic complex between CMT and AOT at the aqueous/organic interface between AOT and CMT, thereby leading to the formation of a hydrophobic species that partitions into the organic phase. Consistent with this mechanism, the efficiency of extraction is dependent on the interfacial mass transfer, the concentrations of CMT and AOT in the aqueous and organic phases, respectively; the ionic strength of the aqueous phase; and the presence of various cosolvents. (c) 1994 John Wiley & Sons, Inc.
Energy-efficient distributed carbon capture in hydrogen production from natural gas (2011)

Lowering the energy penalty associated with CO2 capture is one of the key issues of Carbon Capture and Storage (CCS) technologies. The efficiency of carbon capture must be improved to reduce the energy penalty because capture stage is the most energy-consuming stage in the entire process of CCS. Energy-efficient distributed carbon capture in hydrogen production has been demonstrated with an advanced membrane reformer system. We have already developed and operated an advanced 40 Nm3/h-class membrane reformer system and demonstrated its high hydrogen production efficiency of 81.4% (HHV), which is the world highest efficiency in terms of hydrogen production from natural gas. The system has another significant feature that the CO2 concentration in the reactor off-gas is as high as 70∼90% and CO2 can be liquefied and separated easily with little energy loss. An apparatus for CO2 capture was combined to the membrane reformer system and over 90% of CO2 in the reactor off-gas was captured by cryogenic separation. The total energy efficiency of hydrogen production even with CO2 capture was still as high as 78.6% (HHV), which is 5∼10% higher than the conventional reforming technologies. The total CO2 emission from hydrogen production was decreased by 50% with only a 3% energy loss. A sensitivity analysis was also carried out to evaluate the effects of the operating conditions of the system on hydrogen production efficiency and CO2 reduction rate.
Nonuniform distribution of glucosinolates in Arabidopsis thaliana leaves has important consequences for plant defense (2008)

The spatial distribution of plant defenses within a leaf may be critical in explaining patterns of herbivory. The generalist lepidopteran larvae, Helicoverpa armigera (the cotton bollworm), avoided the midvein and periphery of Arabidopsis thaliana rosette leaves and fed almost exclusively on the inner lamina. This feeding pattern was attributed to glucosinolates because it was not evident in a myrosinase mutant that lacks the ability to activate glucosinolate defenses by hydrolysis. To measure the spatial distribution of glucosinolates in A. thaliana leaves at a fine scale, we constructed ion intensity maps from MALDI-TOF (matrix assisted laser desorption/ionization-time of flight) mass spectra. The major glucosinolates were found to be more abundant in tissues of the midvein and the periphery of the leaf than the inner lamina, patterns that were validated by HPLC analyses of dissected leaves. In addition, there were differences in the proportions of the three major glucosinolates in different leaf regions. Hence, the distribution of glucosinolates within the leaf appears to control the feeding preference of H. armigera larvae. The preferential allocation of glucosinolates to the periphery may play a key role in the defense of leaves by creating a barrier to the feeding of chewing herbivores that frequently approach leaves from the edge.
Structure-function correlations derived from faster variants of a RNA ligase deoxyribozyme (2004)

We previously reported the in vitro selection of several Mg2+-dependent deoxyribozymes (DNA enzymes) that synthesize a 2'-5' RNA linkage from a 2',3'-cyclic phosphate and a 5'-hydroxyl. Here we subjected the 9A2 deoxyribozyme to re-selection for improved ligation rate. We found two new DNA enzymes (7Z81 and 7Z48) that contain the catalytic core of 7Q10, a previously reported small deoxyribozyme that is unrelated in sequence to 9A2. A third new DNA enzyme (7Z101) is unrelated to either 7Q10 or 9A2. The new 7Z81 and 7Z48 DNA enzymes have ligation rates over an order of magnitude higher than that of 7Q10 itself and they have additional sequence elements that correlate with these faster rates. Our findings provide insight into structure-function relationships of catalytic nucleic acids.
Delta-like 4 is the essential, nonredundant ligand for Notch1 during thymic T cell lineage commitment (2008)

Thymic T cell lineage commitment is dependent on Notch1 (N1) receptor-mediated signaling. Although the physiological ligands that interact with N1 expressed on thymic precursors are currently unknown, in vitro culture systems point to Delta-like 1 (DL1) and DL4 as prime candidates. Using DL1- and DL4-lacZ reporter knock-in mice and novel monoclonal antibodies to DL1 and DL4, we show that DL4 is expressed on thymic epithelial cells (TECs), whereas DL1 is not detected. The function of DL4 was further explored in vivo by generating mice in which DL4 could be specifically inactivated in TECs or in hematopoietic progenitors. Although loss of DL4 in hematopoietic progenitors did not perturb thymus development, inactivation of DL4 in TECs led to a complete block in T cell development coupled with the ectopic appearance of immature B cells in the thymus. These immature B cells were phenotypically indistinguishable from those developing in the thymus of conditional N1 mutant mice. Collectively, our results demonstrate that DL4 is the essential and nonredundant N1 ligand responsible for T cell lineage commitment. Moreover, they strongly suggest that N1-expressing thymic progenitors interact with DL4-expressing TECs to suppress B lineage potential and to induce the first steps of intrathymic T cell development.
Measurement of oxygen consumption of rat bone marrow cells by a polarographic method (1968)

Page 751: R. M. Gesinski, J. H. Morrison, and J. R. Toepfer. “Measurement of oxygen consumption of rat bone marrow cells by a polarographic method.” An incorrect value for the Bunsen coefficient was used in calculating oxygen consumption. All values given for microliters of oxygen consumed—in the text, figures, and all tables—should be corrected by dividing by a factor of 4.77. This correction does not alter the interpretations made in the paper but only the magnitude of the consumption reported.
Recent Advances in the Design and Development of Novel Negative Allosteric Modulators of mGlu5 (2011)

Negative allosteric modulators (NAMs) of metabotropic glutamate receptor subtype 5 (mGlu(5)) have remained attractive to researchers as potential therapies for a number of central nervous system related diseases, including anxiety, pain, gastroesophageal reflux disease (GERD), addiction, Parkinson's disease (PD), and fragile X syndrome (FXS). In addition to the many publications with supportive preclinical data with key tool molecules, recent positive reports from the clinic have bolstered the confidence in this approach. During the two year time span from 2009 through 2010, a number of new mGlu(5) NAM chemotypes have been disclosed and discussed in the primary and patent literature. A summary of several efforts representing many diverse chemotypes are presented here, along with a discussion of representative structure activity relationships (SAR) and synthetic approaches to the templates where possible.
Closed-Loop Control of Artificial Pancreatic $\beta$ -Cell in Type 1 Diabetes Mellitus Using Model Predictive Iterative Learning Control (2009)

A novel combination of iterative learning control (ILC) and model predictive control (MPC), referred to here as model predictive iterative learning control (MPILC), is proposed for glycemic control in type 1 diabetes mellitus. MPILC exploits two key factors: frequent glucose readings made possible by continuous glucose monitoring technology; and the repetitive nature of glucose-meal-insulin dynamics with a 24-h cycle. The proposed algorithm can learn from an individual's lifestyle, allowing the control performance to be improved from day to day. After less than 10 days, the blood glucose concentrations can be kept within a range of 90-170 mg/dL. Generally, control performance under MPILC is better than that under MPC. The proposed methodology is robust to random variations in meal timings within ±60 min or meal amounts within ±75% of the nominal value, which validates MPILC's superior robustness compared to run-to-run control. Moreover, to further improve the algorithm's robustness, an automatic scheme for setpoint update that ensures safe convergence is proposed. Furthermore, the proposed method does not require user intervention; hence, the algorithm should be of particular interest for glycemic control in children and adolescents.
The prevalence of a non-phospholipid-binding form of beta2-glycoprotein I in human plasma--consequences for the development of anti-beta2-glycoprotein I antibodies. (1998)

The presence of antiphospholipid antibodies (aPL) is strongly correlated with venous and arterial thrombosis, fetal loss and thrombocytopenia. This relation is called the antiphospholipid syndrome (APS). It is well recognized that thrombosis related aPL are not directed against phospholipids alone, but to phospholipid bound plasma proteins like beta2-glycoprotein I (beta2GPI). aPL that need beta2GPI for the binding to negatively charged phospholipids are called anti-beta2GPI-antibodies. Recently, a mutation in the gene encoding beta2GPI has been described, which results in an amino acid substitution Trp316 into Ser316. This Ser316-beta2GPI did not bind to negatively charged phospholipids. Because only phospholipid bound beta2GPI is recognized by human anti-beta2GPI-antibodies, it might be argued that individuals carrying the Trp316Ser mutation are protected against the development of anti-beta2GPI-antibodies. To investigate this hypothesis, the prevalence of the Trp316Ser mutation was measured in 170 systemic lupus erythematosus (SLE) patients and in 18 patients with the primary antiphospholipid syndrome (PAPS) and the mutation was correlated with the presence of anti-beta2GPI-antibodies. In the total patient group 1 homozygous patient and 21 heterozygous patients were found. The allele frequency of the mutation in SLE patients with anti-beta2GPI-antibodies (0.063) was comparable to that found in SLE patients without anti-beta2GPI-antibodies (0.062). These results indicate that the heterozygous presence of Trp316Ser mutation does not prevent an individual from developing anti-beta2GPI-antibodies. We showed that this can be explained by the concentration of Trp316-beta2GPI in heterozygous patients, which is far above the minimal beta2GPI level necessary for optimal phospholipid binding. In our single patient homozygous for the Trp316Ser mutation no binding beta2GPI to the phospholipid surface was detected and no anti-beta2GPI-antibodies were present in the plasma of this patient. In conclusion, heterozygous Trp316Ser beta2GPI persons are not protected against the development of anti-beta2GPI-antibodies. To confirm that homozygotes do not develop anti-beta2GPI-antibodies a very large population is needed, due to the relatively low prevalence of the mutation.
Effect of p53 Status on Tumor Response to Antiangiogenic Therapy (2002)

The p53 tumor suppressor gene is inactivated in the majority of human cancers. Tumor cells deficient in p53 display a diminished rate of apoptosis under hypoxic conditions, a circumstance that might reduce their reliance on vascular supply, and hence their responsiveness to antiangiogenic therapy. Here, we report that mice bearing tumors derived from p53(-/-) HCT116 human colorectal cancer cells were less responsive to antiangiogenic combination therapy than mice bearing isogenic p53(+/+) tumors. Thus, although antiangiogenic therapy targets genetically stable endothelial cells in the tumor vasculature, genetic alterations that decrease the vascular dependence of tumor cells can influence the therapeutic response of tumors to this therapy.
VeCure: A practical security framework to protect the CAN bus of vehicles (2014)

Vehicles are being revolutionized by integrating modern computing and communication technologies in order to improve both user experience and driving safety. As a result, vehicular systems that used to be closed systems are opening up various interfaces, such as Bluetooth, 3G/4G, GPS, etc., to the outside world, thus introducing new opportunities for cyber attacks. It has been recently demonstrated that modern vehicles are vulnerable to several remote attacks launched through Bluetooth and cellular interfaces, allowing the attacker to take full control of the vehicle. The common root cause of these attacks is the lack of message authentication for the vehicle's internal bus system, called Controller Area Network (CAN). In this work, we propose VeCure - a practical security framework for vehicular systems, which can fundamentally solve the message authentication issue of the CAN bus. VeCure is designed to be compatible with existing vehicle system architectures, and employs a trust group structure and a novel message authentication scheme with offline computation capability to minimize online message processing delay and deployment cost. We built a proof-of-concept prototype on a testbed using Freescale's automotive development boards. The experimental results show that VeCure only introduces 50us additional delay to process a message, which is at least 20-fold faster than any existing solution.
Is bigger better? An argument for very low starting doses (2010)

For years, we and others have advocated starting treatment of chronic indolent conditions at doses lower than those typically recommended in the product monographs.[1][1] The approach we recommend is to use a very low dose when starting a new medication if the condition is not life-threatening or
Solution structure of the potassium channel inhibitor agitoxin 2: Caliper for probing channel geometry (1995)

The structure of the potassium channel blocker agitoxin 2 was solved by solution NMR methods. The structure consists of a triple-stranded antiparallel beta-sheet and a single helix covering one face of the beta-sheet. The cysteine side chains connecting the beta-sheet and the helix form the core of the molecule. One edge of the beta-sheet and the adjacent face of the helix form the interface with the Shaker K+ channel. The fold of agitoxin is homologous to the previously determined folds of scorpion venom toxins. However, agitoxin 2 differs significantly from the other channel blockers in the specificity of its interactions. This study was thus focused on a precise characterization of the surface residues at the face of the protein interacting with the Shaker K+ channel. The rigid toxin molecule can be used to estimate dimensions of the potassium channel. Surface-exposed residues, Arg24, Lys27, and Arg31 of the beta-sheet, have been identified from mutagenesis studies as functionally important for blocking the Shaker K+ channel. The sequential and spatial locations of Arg24 and Arg31 are not conserved among the homologous toxins. Knowledge on the details of the channel-binding sites of agitoxin 2 formed a basis for site-directed mutagenesis studies of the toxin and the K+ channel sequences. Observed interactions between mutated toxin and channel are being used to elucidate the channel structure and mechanisms of channel-toxin interactions.
Bias-switchable dual-band HgCdTe infrared photodetector (1992)

The feasibility of an all molecular-beam epitaxially (MBE) grown, bias-switchable, dual-band HgCdTe detector is demonstrated. Detection in the midwavelength infrared (MWIR) band only or the long-wavelength band (LWIR) only is accomplished by the proper selection of detector bias in the ≥±100 mV range. The devices were all grown in situ by the MBE on CdZnTe or GaAs substrates and consisted of three intentionally doped layers in an n–p–n sequence. At 77 K the floating base two terminal devices responded to the ∼4.9–8 μm spectral band with the application of ≥−100 mV to the bottom contact and to the ∼2.1–4.9 μm band with the application of ≥0 mV. Quantum efficiency depended on bias with a maximum of 59% for LWIR and 66% for MWIR wavelengths at −150 mV and ≥0 mV, respectively. The operation of the dual-band detector is discussed. Significant design differences between the heterojunction phototransistor and the dual-band detector are noted.
Effects of High-Frequency Stimulation on Subthalamic Neuronal Activity in Parkinsonian Patients (2004)

The beneficial effects of high-frequency stimulation result from a change in the firing pattern of cellular discharge and a blockade of the spontaneous overactivity of STN neurons.
Identification of a Distinct, Cryptic Heparosan Synthase from Pasteurella multocida Types A, D, and F (2004)

The extracellular polysaccharide capsules of Pasteurella multocida types A, D, and F are composed of hyaluronan, N-acetylheparosan (heparosan or unsulfated, unepimerized heparin), and unsulfated chondroitin, respectively. Previously, a type D heparosan synthase, a glycosyltransferase that forms the repeating disaccharide heparosan backbone, was identified. Here, a approximately 73% identical gene product that is encoded outside of the capsule biosynthesis locus was also shown to be a functional heparosan synthase. Unlike PmHS1, the PmHS2 enzyme was not stimulated greatly by the addition of an exogenous polymer acceptor and yielded smaller- molecular-weight-product size distributions. Virtually identical hssB genes are found in most type A, D, and F isolates. The occurrence of multiple polysaccharide synthases in a single strain invokes the potential for capsular variation.
Genetic analysis of the activation domain of bovine papillomavirus protein E2: its role in transcription and replication (1996)

The bovine papillomavirus protein E2 serves dual functions in viral transcription and in the initiation of viral replication. As a transcription factor, E2 can cooperatively interact with cellular proteins such as SP1 and stimulate transcription of distal promoters. In replication, E2 and the helicase El are the only viral proteins required for accurate replication of templates containing the viral origin. The amino terminus of E2 is a functionally separable domain critical for activation of both replication and transcription; its primary sequence is conserved between many strains of papillomavirus. We targeted conserved residues spanning the activation domain and constructed a series of 30 amino acid substitution mutants. These mutant E2 genes were analyzed for the ability to activate DNA replication and gene expression in cells. The majority of the substitutions affected the ability of E2 to support both viral replication and transcriptional activation, revealing substantial overlap of the functional determinants for these two processes. Replication and transcription activities are genetically separable, however, as mutations at amino acids 73 and 74 retained replication function but failed to activate transcription. Additionally, a mutation at position 39 substantially reduced replication activity but left transcriptional activation intact. Interestingly, over two-thirds of the mutations analyzed reduced function and protein accumulation, many in a temperature-dependent manner. The correspondence between the replication and transcription phenotypes of mutations spanning the activation domain may indicate that the entire region is folded into a single domain required for both functions.
Photoswitches: From Molecules to Materials (2010)

Small organic molecules, capable of undergoing efficient and reversible photochemical reactions to switch them between (at least) two (meta)stable isomers associated with markedly different properties, continue to impact the materials world. Such photoswitches are being implemented in a variety of materials for applications ranging from optical devices to "smart" polymers. All approaches exploit the photoswitching molecular entities as gates, which translate an incoming light stimulus to trigger macroscopic property changes of the materials. In this progress report, the most promising recent examples in this field are highlighted and put in perspective. Moving from supramolecular systems in solution to surfaces and finally to bulk materials, important design concepts are discussed, emphasizing both the challenges as well as the great promise of such truly advanced materials.
Architecture of gelatin gels (1988)

Abstract The aim of this paper is to make a statement of the present knowledge of the gelation mechanisms of a polymeric, physical gel: the gelatin gel. The description of the system includes both the microscopic and the supramolecular scales. It is shown that the use of different experimental approaches (polarimetry, electron microscopy, rheology) provides complementary views of the phenomenon. The gelation process is presented within the theoretical context of the scaling laws, which establish an analogy with a second-order phase transition. This analogy is illustrated in the case of the gelatin gel, and its implications, with a unified description of gelation in view, are underlined.