gebhart/patrepeval huggingface dataset:
Negative electrostatic surface potential of protein sites specific for anionic ligands. (1996)

Determination of the crystal structure of an "open" unliganded active mutant (T141D) form of the Escherichia coli phosphate receptor for active transport has allowed calculation of the electrostatic surface potential for it and two other comparably modeled receptor structures (wild type and D137N). A discovery of considerable implication is the intensely negative potential of the phosphate-binding cleft. We report similar findings for a sulfate transport receptor, a DNA-binding protein, and, even more dramatically, redox proteins. Evidently, for proteins such as these, which rely almost exclusively on hydrogen bonding for anion interactions and electrostatic balance, a noncomplementary surface potential is not a barrier to binding. Moreover, experimental results show that the exquisite specificity and high affinity of the phosphate and sulfate receptors for unions are insensitive to modulations of charge potential, but extremely sensitive to conditions that leave a hydrogen bond donor or acceptor unpaired.
A Putative Bacterial ABC Transporter Circumvents the Essentiality of Signal Peptidase (2016)

The type I signal peptidase of Staphylococcus aureus (SpsB) enables the secretion of numerous proteins by cleavage of the signal peptide. We synthesized an SpsB inhibitor with potent activity against various clinical S. aureus strains. The predominant S. aureus strain USA300 develops resistance to this inhibitor by mutations in a novel transcriptional repressor (cro/cI), causing overexpression of a putative ABC transporter. This mechanism promotes the cleavage and secretion of various proteins independently of SpsB and compensates for the requirement of SpsB for viability in vitro However, bacteria overexpressing the ABC transporter and lacking SpsB secrete reduced levels of virulence-associated proteins and are unable to infect mice. This study describes a bacterial resistance mechanism that provides novel insights into the biology of bacterial secretion.
Expression of the mouse dihydrofolate reductase complementary deoxyribonucleic acid in simian virus 40 vectors. (1981)

A mouse complementary deoxyribonucleic acid segment coding for the enzyme dihydrofolate reductase has been cloned in two general classes of vectors containing simian virus 40 deoxyribonucleic acid: (i) those that can be propagated as virions in permissive cells and (ii) those that can be introduced into and maintained stably in various mammalian cells. Both types of vectors express the mouse dihydrofolate reductase by using signals supplied by simian virus 40 deoxyribonucleic acid sequences. Moreover, plasmid vectors carrying the complementary deoxyribonucleic acid segment can complement Chinese hamster ovary cells lacking dihydrofolate reductase.
Production of Phenylacetic and Hydroxyphenylacetic Acids by Clostridium botulinum Type G (1980)

Phenylacetic and hydroxyphenylacetic acids were present as major acids in spent growth medium from Clostridium botulinum type G. These aromatic acids were identified by gas-liquid chromatography and mass spectrometry.
IP-10 Blocks Vascular Endothelial Growth Factor-Induced Endothelial Cell Motility and Tube Formation via Inhibition of Calpain (2006)

Angiogenesis plays a critical role in wound repair. Endothelial cells present CXC receptor 3 (CXCR3) for chemokines expressed late in wound regeneration. To understand the physiological role CXCR3 plays in regulating endothelial function, we analyzed the ability of a CXCR3 ligand, IP-10 (CXCL10), to influence endothelial cell tube formation. Treatment of endothelial cells with IP-10 in the presence of vascular endothelial growth factor (VEGF) inhibited tube formation on growth factor-reduced Matrigel and in a subcutaneous Matrigel plug. Furthermore, IP-10 significantly inhibited VEGF-induced endothelial motility, a response critical for angiogenesis. Previous work showed that CXCR3 ligandation initiates protein kinase A (PKA) phosphorylation-dependent inhibition of m-calpain, required for induced cell motility, in fibroblasts but not epithelial cells. Here we show that CXCR3 activation in endothelial cells induces an increase in cAMP and PKA activation. Treatment of endothelial cells with Rp-8-Br-cAMP, an inhibitor of PKA, or small interference RNA to PKA was able to reverse the inhibitory effects of IP-10 on VEGF-mediated tube formation and motility. Importantly, treatment of endothelial cells with VEGF induced the activation of m-calpain, but costimulation with IP-10 significantly decreased this activity. Using Rp-8-Br-cAMP, we show blocking PKA reversed the IP-10 inhibition of VEGF-induced m-calpain activity. These data indicate that the activation of CXCR3 inhibits endothelial tube formation through a PKA mediated inhibition of m-calpain. This provides a means by which late wound repair signals limit the angiogenesis driven early in the wound response process.
Regulation of Germline Promoters by the Two Human Ig Heavy Chain 3′ α Enhancers (2000)

The human IgH 3' enhancers, located downstream of each of the two Calpha genes, modulate germline (GL) transcription of the IgH genes by influencing the activity of promoter-enhancer complexes upstream of the switch and intervening (I) regions. The regulation of GL alpha1 and alpha2 promoters by different human 3' enhancer fragments was investigated in cell lines representing various developmental stages. Both alpha1HS1,2 and alpha2HS1,2 fragments show equally strong enhancer activity on the GL alpha1 and alpha2 promoters in both orientations when transiently transfected into a number of mature B cell line (DG75, CL-01, and HS Sultan). However, there is no activity in a human pre-B cell line (NALM-6) nor a human T cell line (Jurkat). HS3 shows no enhancer activity by itself in any of the cell lines, whereas a modest effect is noted using HS4 in the three mature B cell lines. However, the combination of the alpha2HS3-HS1,2-HS4 fragments, which together form a potential locus control region, displays a markedly stronger enhancer activity than the individual fragments with a differential effect on the alpha1 and alpha2 promoters as compared with the gamma3 promoter. Our results suggest that the human GL alpha promoter may be regulated by two independent pathways. One pathway is induced by TGF-beta1 which directs IgA isotype switch through activation of the GL alpha promoter and no TGF-beta1-responsive elements are present in the different 3' enhancer fragments. The other route is through the human 3' enhancer regions that cis-up-regulate the GL alpha promoter activity in mature B cells.
[Calcitonin gene-related peptide (CGRP): a vasodilator neuropeptide with many potential applications]. (1993)

CGRP (calcitonin gene-related peptide) is a potent vasodilator neuropeptide which acts on peri-arteriolar neurones and is implicated in the pathogenesis of numerous cardiovascular diseases. The synthesis of CGRP antagonists should be useful for the treatment of Raynaud's disease as well as migraine. There exists an homology between the structures of CGRP and pancreatic amylin and therefore an eventual role of CGRP in type II diabetes pathophysiology is currently being studied.
Schizophrenia: Improving Outcome (1999)

Therapeutic advances over the last four decades have enabled most persons with schizophrenia to live in the community. Nevertheless, the majority will continue to experience various symptoms and to have social and cognitive disabilities. With the development of new medications and psychosocial interventions, outpatient status can no longer be viewed as a satisfactory final outcome. This article presents the current state of schizophrenia therapeutics in a variety of clinically relevant situations: first-episode psychosis, treatment-resistant psychosis, chronic, relapsing psychosis, continuous poor functioning, and chronic psychosis not responsive to pharmacotherapy. The first-line atypical antipsychotics should generally be used, mainly because of their comparatively benign side-effect profiles, and they should be given as early as possible in the illness. The clinician should not be quick to accept persistent psychosis; the second-line atypical clozapine should be tried early in the course of the disease in patients showing treatment resistance. For patients residing with their families, educational and supportive family interventions have an important effect on relapse prevention; for those who live on their own and suffer frequent relapses, Assertive Community Treatment may be helpful. Patients with psychosis that is not responsive to pharmacotherapy may benefit from specific modalities of cognitive-behavioral therapy currently being developed, while persons with persistent negative symptoms and limited social competence may find social-skills training useful. In addition, new programs of supported employment may enable some patients to maintain competitive employment.
11 Anterior Excision and Vertebral Body Fusion Operation for Intervertebral Disk Syndromes of the Lower Lumbar Spine (1963)

Fig. 10 Halftone drawings, demonstrating a transvertebral grafting procedure on the anterior aspect of the lumbosacral joint. The lower right-hand figure shows insertion of full -thickness iliac graft, ‘‘coin’’ type. Two such grafts per level are preferred. If the most superficial (ventral) graft cannot be countersunk to more than one-eighth inch below the vertebral margin, screw fixation, oblique at a 45-degree angle through graft and into sacral body is recommended. (Reprinted with permission and Lippincott Williams & Wilkins, from Harmon, PH. Anterior excision and vertebral body fusion operation for intervertebral disk syndromes of the lower lumbar spine: three to five year results in 244 cases. Clin Orthop Relat Res. 1963;26:107–127.) Fig. 11 An alternative technique of preparation of graft bed and insertion of 2 rectangular grafts illustrated for the L-4 level: (A) incision in the anterior ligament; (B) preparation of graft bed; (C) completed grafting procedure. (Reprinted with permission and Lippincott Williams & Wilkins, from Harmon, PH. Anterior excision and vertebral body fusion operation for intervertebral disk syndromes of the lower lumbar spine: three to five year results in 244 cases. Clin Orthop Relat Res. 1963;26:107–127.) Published online: 31 March 2012 The Association of Bone and Joint Surgeons1 2012
Activated T cells Inhibit NK Cell‐mediated Tumour Rejection (2009)

Previous studies have described the regulation of some T-cell subsets toward natural killer (NK) cells. Naturally occurring CD4(+)CD25(+) T regulatory cells can inhibit NK cell cytotoxicity, while activated interleukin-2 (IL-2) secreting T cells can stimulate NK cells. However, little is known about the impact of the integrity T-cell population on the final outcome of NK cell cytotoxicity. We thus examined the possible role of activated T cells in affecting NK cell cytotoxicity by mixed lymphocyte co-cultures in vitro and a B16 melanoma tumour model in vivo. In our study, activated T cells were found to be able to significantly inhibit NK cell cytotoxicity in vitro and blunt NK cell-mediated tumour rejection in vivo. The inhibition of NK cell function is a cell-cell contact dependent way. Results suggest that activated T cells may play an important role in limiting NK cell functions, which might be very significant for the design of biotherapy against tumour or infection in future.
Murine embryonic stem cell differentiation is promoted by SOCS-3 and inhibited by the zinc finger transcription factor Klf4 (2004)

Embryonic stem (ES) cells homozygous for a Shp-2 mutation (Shp-2(Delta46-110)) demonstrate leukemia inhibitory factor (LIF) hypersensitivity and increased LIF-stimulated phosphorylation of signal transducer and activator of transcription (STAT3). We hypothesized that LIF-responsive genes in Shp-2(Delta46-110) cells would represent potential candidates for molecules vital for ES cell self-renewal. Using microarray analysis, we detected 41 genes whose expression was modified by LIF in Shp-2(Delta46-110) ES cells. Induction of 2 significantly up-regulated genes, suppressor of cytokine signaling-3 (SOCS-3) and Kruppel-like factor 4 (Klf4), was verified using Northern blotting. ES cells overexpressing SOCS-3 had an increased capacity to differentiate to hematopoietic progenitors, rather than to self-renew. In contrast, ES cells overexpressing Klf4 had a greater capacity to self-renew based on secondary embryoid body (EB) formation. Klf4-transduced d6 EBs expressed higher levels of Oct-4, consistent with the notion that Klf4 promotes ES cell self-renewal. These findings verify the negative role of SOCS-3 on LIF signaling and provide a novel role for Klf4 in ES cell function.
Nucleator-dependent intercellular assembly of adhesive curli organelles in Escherichia coli. (1996)

Bacterial adhesion to other bacteria, to eukaryotic cells, and to extracellular matrix proteins is frequently mediated by cell surface-associated polymers (fimbriae) consisting of one or more subunit proteins. We have found that polymerization of curlin to fimbriae-like structures (curli) on the surface of Escherichia coli markedly differs from the prevailing model for fimbrial assembly in that it occurs extracellularly through a self-assembly process depending on a specific nucleator protein. The cell surface-bound nucleator primes the polymerization of curlin secreted by the nucleator-presenting cell or by adjacent cells. The addition of monomers to the growing filament seems to be driven by mass action and guided only by the diffusion gradient between the source of secreted monomer and the surface of monomer condensation.
Cushing's Syndrome (1995)

Cushing's syndrome is usually caused by the secretion of corticotropin or cortisol by a pituitary or adrenal tumor, respectively, or by ectopic secretion of corticotropin. It is possible to determine the specific abnormality in most patients, but it can sometimes be difficult to decide whether the patient has hypercortisolism and whether it is primary or due to major depressive disorder or to the stress of other diseases. Determining the cause of the hypercortisolism involves performing multiple tests in a logical sequence; the results should all be consistent with the same diagnosis. Treatment should aim to cure the hypercortisolism and to eliminate any tumor that threatens the patient's health, while minimizing the chance of an endocrine deficiency or long-term dependence on medications.
Notch signaling controls liver development by regulating biliary differentiation (2009)

In the mammalian liver, bile is transported to the intestine through an intricate network of bile ducts. Notch signaling is required for normal duct formation, but its mode of action has been unclear. Here, we show in mice that bile ducts arise through a novel mechanism of tubulogenesis involving sequential radial differentiation. Notch signaling is activated in a subset of liver progenitor cells fated to become ductal cells, and pathway activation is necessary for biliary fate. Notch signals are also required for bile duct morphogenesis, and activation of Notch signaling in the hepatic lobule promotes ectopic biliary differentiation and tubule formation in a dose-dependent manner. Remarkably, activation of Notch signaling in postnatal hepatocytes causes them to adopt a biliary fate through a process of reprogramming that recapitulates normal bile duct development. These results reconcile previous conflicting reports about the role of Notch during liver development and suggest that Notch acts by coordinating biliary differentiation and morphogenesis.
Second-trimester markers of fetal size in schizophrenia: a study of monozygotic twins (1992)

The study suggests that various second-trimester prenatal disturbances in the epigenesis of one twin in a pair discordant for schizophrenia may be related to the fact that only one of the twins expresses his or her genetic predisposition toward schizophrenia. This is consistent with a "two-strike" etiology of schizophrenia: a genetic diathesis plus a second-trimester environmental stressor.
FET diode linearizer optimization for amplifier predistortion in digital radios (2000)

This letter presents the initial results of a study on a diode-based power amplifier (PA) linearization technique. The optimization of a diode's parameters to match a MESFET PA is discussed. The relevance of AM-AM and AM-PM curves to linearity requirements and modulation format is also discussed. As much as a 6.7-dB improvement in ACPR is made in the upper channel using a series diode linearizer.
[Expression of tumor-specific cancer/testis antigens in hepatocellular carcinoma]. (2003)

With a highly conserved coding gene, seven CT antigens were expressed in 20.0% - 70.0% of Chinese HCC patients. CT antigens' expression had correlations with some clinical characters.
Self-Assembling Protein Arrays Using Electronic Semiconductor Microchips and in Vitro Translation (2003)

Protein arrays will greatly accelerate research and development in medical and biological sciences. We have used cell-free protein biosynthesis and a parallel immobilization strategy for producing protein biochips. We demonstrate a model two-protein microarray using luciferase and green fluorescent protein, both expressed in a cell-free system and specifically immobilized on CombiMatrix semiconductor oligonucleotide microarrays. This demonstration provides evidence for the appropriate folding, activity, robust presentation, and efficient flexible detection of proteins on the microscale.
How to obey the 7 commandments for natural language dialogue (1996)

In this paper we will describe the design of the dialogue management module for a voice-operated system for car driver information. The literature on designing 'good' user interfaces\ninvolving natural language dialogue in general and spoken language in particular abounds\nwith useful guidelines for actual development. We have tried to summarize these guidelines\nin 7 'commandments'. Trying to obey these 7 commandments when designing a system to be used in 'ordinary' situations is by no means easy. To obey them when designing systems for in-car usage is even more difficult: the noisy environment increases the possibility for speech recognition errors, the driver has to perform several other tasks while communicating with the system, etc. In this paper, we will discuss how these constraints influence the design of the dialogue management module and how the additional requirements fit in with the 7 commandments.
Adsorption of biopolymers at hydrophilic cellulose–water interface (2005)

The extent of adsorption (Gamma2(1)) of bovine serum albumin (BSA), beta-lactoglobulin, lysozyme, gelatin, and DNA from aqueous solution onto the hydrophilic surface of cellulose has been measured as function of biopolymer concentration at different temperatures, pHs, and ionic strengths, and in the presence of a high concentration of inorganic salts and denaturants. In all cases, the value of Gamma2(1) increases with the increase of biopolymer concentration (X2) in bulk and it attains a maximum value at a critical mole fraction concentration X2m. The value of Gamma2m depends upon the nature of protein, temperature, pH, and ionic strength, as well as the nature of neutral salts present in excess. Gamma2m for proteins at a fixed physicochemical condition stands in the following order: Gelatin>betalactoglobulin>lysozyme>BSA. The isotherms for adsorption of DNA nucleotides on cellulose surface at pH 4.0 have been compared at different temperatures and ionic strengths, and in the presence of high concentration of inorganic salts LiCl, NaCl, KCl, and Na2SO4. Values of Gamma2m for different systems have been evaluated and critically compared. At pH 6.0 and 8.0, Gamma2(1) values of DNA nucleotides on cellulose are all negative due to the excess positive hydration of cellulose. At pH 4.0, adsorption of nucleotides of acid, alkali, and heat-denatured DNA widely differ from each other and in the presence of excess concentration of urea becomes negative. The probable mechanisms of biopolymer-cellulose adsorption in terms of polymer hydration, steric interaction, London-van der Waals, hydrophobic, and other types of interactions have been discussed qualitatively. The standard free energy change for the adsorption of protein and DNA nucleotides on the cellulose surface at the state of adsorption saturation has been calculated in kJ per kg of cellulose using an integrated form of the Gibbs adsorption equation. The relation between DeltaG degrees and maximum affinities between biopolymers and the polysaccharide interface have been discussed for various systems.
Lupus and Epstein-Barr (2012)

Recent advances demonstrate SLE-specific serologic responses, gene expression, viral load, T-cell responses, humoral fine specificity, and molecular mimicry with EBV, further supporting potential roles for EBV in lupus etiology and pathogenesis.
Spatial and temporal dependence of interspark interactions in femtosecond-nanosecond dual-pulse laser-induced breakdown spectroscopy (2004)

A femtosecond air spark has recently been combined with a nanosecond ablative pulse in order to map the spatial and temporal interactions of the two plasmas in femtosecond-nanosecond orthogonal preablation spark dual-pulse laser-induced breakdown spectroscopy (LIBS). Good spatial and temporal correlation was found for reduced atomic emission from atmospheric species (nitrogen and oxygen) and increased atomic emission from ablated species (copper and aluminum) in the femtosecond-nanosecond plasma, suggesting a potential role for atmospheric pressure or nitrogen/oxygen concentration reduction following air spark formation in generating atomic emission enhancements in dual-pulse LIBS.
Reversal of hyperreactivity to bradykinin in renal hypertensive rats. (1990)

Increased blood pressure responsiveness to bradykinin in comparison with other vasodilator agents was demonstrated in rats with long-term one-kidney and two-kidney, one clip hypertension. In the present study, we analyzed the reactivity to intra-aortically injected bradykinin in unanesthetized one-kidney, one clip hypertensive rats during the control period and 1, 5, and 8 hours after reversal of hypertension after removal of the renal artery constriction. One and 5 hours after unclipping the renal artery, the mean blood pressure decreased markedly (from 195 +/- 7 to 124 +/- 8 and 145 +/- 9 mm Hg, respectively), whereas the hyperreactivity to bradykinin reverted only slightly, and the responses to nitroprusside remained unchanged. In another group of hypertensive rats examined 8 hours after unclipping (pressure decreased from 192 +/- 4 to 143 +/- 8 mm Hg), the hyperreactivity to bradykinin had partially reverted. Significantly larger doses of bradykinin were necessary to produce the same decrease in blood pressure when compared with the control period (16.4 +/- 2.0 vs. 7.2 +/- 1.2 ng). The same degree of reversal of hyperreactivity to bradykinin was observed when the blood pressure of hypertensive rats was reduced (from 207 +/- 8 to 143 +/- 5 mm Hg) during 1 hour by hydralazine injection. Complete reversibility of bradykinin hyperreactivity was produced by nitroprusside infusion (from 201 +/- 13 to 142 +/- 10 mm Hg).(ABSTRACT TRUNCATED AT 250 WORDS)