gebhart/patrepeval huggingface dataset:
Growth Factors and Chronic Wound Healing: Past, Present, and Future (2004)

Growth substances (cytokines and growth factors) are soluble signaling proteins affecting the process of normal wound healing. Cytokines govern the inflammatory phase that clears cellular and extracellular matrix debris. Wound repair is controlled by growth factors (platelet-derived growth factor [PDGF], keratinocyte growth factor, and transforming growth factor beta). Endogenous growth factors communicate across the dermal-epidermal interface. PDGF is important for most phases of wound healing. Becaplermin (PDGF-BB), the only growth factor approved by the Food and Drug Administration, requires daily application for neuropathic wound healing. Gene therapy is under development for more efficient growth factor delivery; a single application will induce constitutive growth factor expression for weeks. Based on dramatic preclinical animal studies, a phase 1 clinical trial planned on a PDGF genetic construct appears promising.
Immunotherapy of patients with advanced cancer using tumor-infiltrating lymphocytes and recombinant interleukin-2: a pilot study. (1988)

Clinical investigations using the adoptive transfer of lymphokine-activated killer (LAK) cells and recombinant interleukin-2 (rIL-2) to treat patients with advanced cancer have yielded encouraging results. We have thus sought ways to enhance the effectiveness of adoptive immunotherapy while minimizing its toxic side effects. Murine experiments have identified tumor-infiltrating lymphocytes (TIL) as killer cells more effective than LAK cells and less dependent on adjunctive systemically administered IL-2 to mediate antitumor effects. Accordingly, we performed a pilot protocol to investigate the feasibility and practicality of administering IL-2-expanded TIL to humans with metastatic cancers. Twelve patients, including six with melanoma, four with renal cell carcinoma, one with breast carcinoma, and one with colon carcinoma, were treated with varying doses and combinations of TIL (8.0 X 10(9) to 2.3 X 10(11) cells per patient), IL-2 (10,000 to 100,000 U/kg three times daily to dose-limiting toxicity), and cyclophosphamide (CPM) (up to 50 mg/kg). Two partial responses (PR) to therapy were observed: pulmonary and mediastinal masses regressed in a patient with melanoma, and a lymph node mass regressed in a patient with renal cell carcinoma. One additional patient with breast cancer experienced a partial regression of disease in lymph nodal and cutaneous sites with complete elimination of malignant cells from a pleural effusion, although cutaneous disease recurred at 4 weeks. The toxicities of therapy were similar to those ascribed to IL-2; no toxic effects were directly attributable to TIL infusions. In five of six melanoma patients, TIL demonstrated lytic activity specific for the autologous tumor target in short-term chromium-release assays, distinct from the nonspecific lytic activity characteristic of LAK cells. This study represents an initial attempt to identify and use lymphocyte subsets with enhanced tumoricidal capacity in the adoptive immunotherapy of human malignancies.
Multilayer Nitroazobenzene Films Covalently Attached to Carbon. An AFM and Electrochemical Study (2005)

Nitroazobenzene films have been grafted to pyrolyzed photoresist films by electrochemical reduction of the corresponding diazonium salt in acetonitrile solution. Two component films were also prepared by electrochemically grafting methylbenzene layers to preformed NAB films. Voltammetric investigation of the films in aqueous acid medium and the measurement of film thickness using atomic force microscopy (AFM) lead to new insights into film structure. In aqueous acid solution, the azobenzene groups have no detectable electroactivity and not all nitro groups in the films can be reduced. These findings point to a compact film structure in which proton diffusion is limited. There may also be spatial inhibition of the conformational changes that accompany azobenzene reduction. For increasingly thick NAB films, the peak for reduction of the nitro groups moves to more negative potentials and the peaks become more asymmetric in shape. These changes are interpreted in terms of the dielectric properties and the rate of proton diffusion in the films. Film thickness was measured by ploughing through the film with an AFM tip. When an NAB film prepared in acetonitrile solution is reduced in aqueous acid, the film thickness decreases by more than 50%. The changes can be partially reversed by treatment in acetonitrile-electrolyte solution and hence are attributed to ion-solvent induced swelling and shrinking. Thus, the large decrease in thickness detected by AFM after treatment of the film in aqueous acid is consistent with the compact film structure revealed by electrochemistry.
Partitioned linear block codes for computer memory with 'stuck-at' defects (1983)

Linear block codes are studied for improving the reliability of message storage in computer memory with stuck-at defects and noise. The case when the side information about the state of the defects is available to the decoder or to the encoder is considered. In the former case, stuck-at cells act as erasures so that techniques for decoding linear block codes for erasures and errors can be directly applied. We concentrate on the complimentary problem of incorporating stuck-at information in the encoding of linear block codes. An algebraic model for stuck-at defects and additive errors is presented. The notion of a "partitioned" linear block code is introduced to mask defects known at the encoder and to correct random errors at the decoder. The defect and error correction capability of partitioned linear block codes is characterized in terms of minimum distances. A class of partitioned cyclic codes is introduced. A BCH-type bound for these cyclic codes is derived and employed to construct partitioned linear block codes with specified bounds on the minimum distances. Finally, a probabilistic model for the generation of stuck-at cells is presented. It is shown that partitioned linear block codes achieve the Shannon capacity for a computer memory with symmetric defects and errors.
Diagnostic assays for HIV-1 infection. (2004)

orldwide, a total 40 million people were estimated to be living with HIV/AIDS through the end of 2003.1 According to the World Health Organization and the Joint United Nations Programme on HIV/ AIDS, over 5 million new infections occurred in 2003, which translates to roughly 14,000 new infections daily. Since the first case of HIV infection was diagnosed in the United States in 1981, there have been an estimated 886,575 AIDS diagnoses through 2002.2,3 Currently, there are an estimated 800,000 to 900,000 persons living with HIV in the United States, with an estimated 40,000 new infections per year.3 The ability to diagnose HIV infection is a critical component in the efforts to stem the continued spread of the epidemic, because knowledge of individual HIV-serostatus can help prevent secondary transmission of infection. Diagnostic assays for HIV infection have evolved substantially since the introduction of antibody testing in 1985. This article summarizes a number of HIV test technologies cleared by the United States Food and Drug Administration (FDA) for diagnostic use in the United States and reviews several recently developed assays that represent further progress in diagnostic technology.
Decarbonylation dehydration of fatty acids to alkenes in the presence of transition metal complexes (1976)

Abstract The catalytic decarbonylation of stearic acid into a mixture of heptadecenes has been accomplished by use of a catalyst system comprised of rhodium trichloride (RhCl 3 ) and triphenylphosphine. The isomeric composition of the heptadecenes formed was found, by spectroscopic and chemical methods, to be dependent upon the type of rhodium catalyst employed. Anhydrous RhCl 3 produced about the same amount of 2‐heptadecene, twice the amount of 3‐heptadecene, and about half the amount of 1‐heptadecene as hydrated RhCl 3 . The active catalytic species formed in situ has been identified as the rhodium I complex [(C 6 H 5 ) 3 P] 2 Rh(CO)Cl. A mechanistic pathway to account for the observed decarbonylation products employing the above catalyst is presented.
Primary characterization of the protein products of the Escherichia coli ompB locus: structure and regulation of synthesis of the OmpR and EnvZ proteins (1985)

The ompB operon of Escherichia coli contains the structural genes for two proteins, OmpR and EnvZ, which control the osmoregulated biosynthesis of the porin proteins OmpF and OmpC. By inserting XbaI octamer linkers into the cloned ompB locus, four distinct frameshift mutants were isolated and subsequently characterized for their OmpR and EnvZ protein products and their outer membrane porin phenotype. In a minicell expression system, the wild-type products of the ompR and envZ genes were found to be approximately 28 and 50 kilodaltons in size, respectively, whereas the mutant proteins were either truncated or extended due to the frame shift. The identity of the envZ gene product was confirmed by immunoprecipitation. M13 dideoxy sequencing of the DNA around the wild-type ompR-envZ junction revealed an error in the sequence published for this operon; the complete corrected sequence is presented. A sequence, ATGA, was found that forms the termination codon for the OmpR reading frame and a possible initiation codon for the EnvZ protein; these sequences are consistent with the sizes of the proteins observed after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The translational activity of this ATG codon was confirmed by fusing the lacZ gene in frame with the putative EnvZ coding sequence. The implications of these results are discussed with respect to the regulation of synthesis of the ompB gene products.
Phase 1 Dose-Escalation Study of CP-690 550 in Stable Renal Allograft Recipients: Preliminary Findings of Safety, Tolerability, Effects on Lymphocyte Subsets and Pharmacokinetics (2008)

CP-690 550 inhibits Janus kinase 3 with nanomolar potency. In this dose-escalation study, we assessed the safety, tolerability, effects on lymphocyte subsets, and pharmacokinetics of CP-690 550 when coadministered with mycophenolate mofetil in stable renal allograft recipients for 28 days. Twenty-eight patients were enrolled. Six patients received CP-690 550 5 mg twice daily (BID), 6 patients received 15 mg BID, 10 patients received 30 mg BID, and 6 patients received placebo. The most frequent adverse events were infections and gastrointestinal (abdominal pain, diarrhea, dyspepsia, and vomiting). CP-690 550 15 mg BID and 30 mg BID were associated with a mean decrease in hemoglobin from baseline of 11% and a mean decrease in absolute natural killer cell counts of 50%. CP-690 550 30 mg BID was also associated with a mean increase in absolute CD19(+) B-lymphocytes of 130%. There were no changes in the number of neutrophils, total lymphocytes, platelets, or CD4(+) or CD8(+) T cells; clinical chemistry; vital signs; or electrocardiograms from the pretreatment baseline. Administration of CP-690 550 without a concomitant calcineurin inhibitor resulted in CP-690 550 exposures consistent with previous studies in nontransplant subjects. Additional dose-ranging studies are warranted to evaluate the safety and efficacy of CP-690 550 in renal transplant recipients over longer treatment duration.
Adult mesenchymal stem cells: characterization, differentiation, and application in cell and gene therapy (2004)

A considerable amount of retrospective data is available that describes putative mesenchymal stem cells (MSCs). However, there is still very little knowledge available that documents the properties of a MSC in its native environment. Although the precise identity of MSCs remains a challenge, further understanding of their biological properties will be greatly advanced by analyzing the mechanisms that govern their self-renewal and differentiation potential. This review begins with the current state of knowledge on the biology of MSCs, specifically with respect to their existence in the adult organism and postulation of their biological niche. While MSCs are considered suitable candidates for cell-based strategies owing to their intrinsic capacity to self-renew and differentiate, there is currently little information available regarding the molecular mechanisms that govern their stem cell potential. We propose here a model for the regulation of MSC differentiation, and recent findings regarding the regulation of MSC differentiation are discussed. Current research efforts focused on elucidating the mechanisms regulating MSC differentiation should facilitate the design of optimal in vitro culture conditions to enhance their clinical utility cell and gene therapy.
Galvanic Deposition of Nanostructured Noble-Metal Films on Silicon (2005)

Large-area nanostructured noble-metal films (Ag, Pt, and Au) can be deposited with high yields and various morphologies on silicon formed between the semiconductor and the noble metal by means of a galvanic cell. It is shown that the morphology of Ag, which is different from that of Pt and Au, can be influenced markedly by the deposition conditions. Distinctive surface-enhanced Raman-scattering features are observed on these Ag films.
Cloning, genetic organization, and characterization of a structural gene encoding bacillopeptidase F from Bacillus subtilis. (1990)

Bacillopeptidase F is an extracellular serine protease that is expressed at the beginning of the stationary phase. To study its structure, regulation of expression, and physiological roles, we have cloned and characterized the structural gene (bpf) encoding this protease from Bacillus subtilis. DNA sequence analysis suggests this protease is synthesized as a preproenzyme (Mr = 92,000). Through processing at both the NH2 and COOH termini, it is gradually converted into various forms with molecular mass ranging from 80 to 48 kDa. Shortening the 3' end of bpf demonstrates that at least 290 amino acid residues from the COOH-terminus of bacillopeptidase F are not required for either catalytic activity or secretion. Bacillopeptidase F exhibits sequence similarity with several serine proteases. Its gene is found immediately downstream from the fts operon which was mapped at 135 degrees on the B. subtilis genetic linkage map. Inactivation of the chromosomal copy of bpf shows no effect on cell growth and sporulation. A triple protease-deficient strain (WB300 with the structural genes for bacillopeptidase F and two other major proteases inactivated) was constructed to serve as a better expression host for the production and secretion of foreign proteins.
Evaluation of H2O2 Prophylaxis of Bacteriuria in Patients with Long-Term Indwelling Foley Catheters: A Randomized Controlled Study (1985)

Abstract Since the long-term catheterized patient is at significant risk of urinary tract infection, and the catheter drainage bags of these patients are at significant risk of becoming reservoirs for nosocomial pathogens, we carried out a randomized, controlled study to determine the efficacy of intermittent drainage bag instillation of hydrogen peroxide (H 2 O 2 ) in patients requiring indwelling Foley catheters for 5 days or more. Herein we report the effects of this technique on the rates of catheter and bag bacteriuria, the duration to positive culture, the temporal relationships observed, and the spectrum of organisms recovered. Bag source bacteriuria was found with the same frequency in both control and H 2 O 2 groups. H 2 O 2 did reduce contamination of the drainage bag but did not reduce catheter-associated bacteriuria or frequency of symptomatic urinary tract infection. Furthermore, H 2 O 2 did not reduce the frequency of bag contamination with most of the common nosocomial urinary pathogens.
Numerical Solution of Implicitly Constrained Optimization Problems (2008)

Abstract. Many applications require the minimization of a smooth function f: R nu → R whose evaluation requires the solution of a system of nonlinear equations. This system represents a numerical simulation that must be run to evaluate f. This system of nonlinear equations is referred to as an implicit constraint. In principle f can be minimized using the steepest descent method or Newton-type methods for unconstrained minimization. However, for the practical application of derivative based methods for the minimization of f one has to deal with many interesting issues that arise out of the presence of the implicit constraints that must be solved to evaluate f. This article studies some of these issues, ranging from sensitivity and adjoint techniques for derivative computation to implementation issues in Newton-type methods. A discretized optimal control problem governed by the unsteady Burgers equation is used to illustrate the ideas. The material in this article is accessible to anyone with knowledge of Newton-type methods for finite dimensional unconstrained optimization. Many of the concepts discussed in this article extend to and are used in areas such as optimal control and PDE constrained optimization.
Preclinical characterization of an anti-methamphetamine monoclonal antibody for human use (2013)

Ch-mAb7F9, a human-mouse chimeric monoclonal antibody (mAb) designed to bind (+)-methamphetamine (METH) with high affinity and specificity, was produced as a treatment medication for METH abuse. In these studies, we present the preclinical characterization that provided predictive evidence that ch-mAb7F9 may be safe and effective in humans. In vitro ligand binding studies showed that ch-mAb7F9 is specific for and only binds its target ligands (METH, (+)-amphetamine, and 3,4-methylenedioxy-N-methylamphetamine) with high affinity. It did not bind endogenous neurotransmitters or other medications and was not bound by protein C1q, thus it is unlikely to stimulate in vivo complement-dependent cytotoxicity. Isothermal titration calorimetry potency studies showed that METH binding by ch-mAb7F9 is efficient. Pharmacokinetic studies of METH given after ch-mAb7F9 doses in rats demonstrated the in vivo application of these in vitro METH-binding characteristics. While METH had little effect on ch-mAb7F9 disposition, ch-mAb7F9 substantially altered METH disposition, dramatically reducing the volume of distribution and clearance of METH. The elimination half-life of METH was increased by ch-mAb7F9, but it was still very fast compared with the elimination of ch-mAb7F9. Importantly, the rapid elimination of unbound METH combined with previous knowledge of mAb:target ligand binding dynamics suggested that ch-mAb7F9 binding capacity regenerates over time. This finding has substantial therapeutic implications regarding the METH doses against which ch-mAb7F9 will be effective, on the duration of ch-mAb7F9 effects, and on the safety of ch-mAb7F9 in METH users who use METH while taking ch-mAb7F9. These results helped to support initiation of a Phase 1a study of ch-mAb7F9.
Multimedia synchronization for live presentation using the N-buffer approach (2002)

The demand of bringing multimedia information systems into distributed environments makes multimedia synchronization more difficult. In order to eliminate the side effects which result from delay jitters, we propose a bounded buffer allocation scheme, in which the audio stream adopts the blocking synchronization scheme and the video stream adopts the non-blocking synchronization scheme, for live audio and video presentations in this paper. The forward synchronization schemes are performed to overcome the asynchrony anomalies. Once some anomalies of presentations are detected, a forward re-synchronization scheme is triggered to eliminate the asynchrony anomalies. Neither a global clock nor a feedback mechanism is needed using the proposed method. Based on the proposed method, trade-offs between the presentation qualities and networking resources are mathematically calculated. According to these calculable trade-offs, users can derive their own (acceptable) presentation qualities of live video and live audio media based on their available networking resources.
<title>Preliminary evaluation of collagen as a component in the thermally induced 'weld'</title> (1991)

A simple thermodynamic approach to tissue 'welding' was studied. Fresh bovine tendon (67% type I collagen) was sectioned into disk shaped pieces, pairs of which were inserted between bowed glass coverslips and wrapped in aluminum foil. The packets were heated in a waterbath according to two protocols. In group I, packets were tested for four minutes at temperatures between 55-65 degree(s)C, in 1 degree(s)C intervals. In group II, the packets were kept at 62 degree(s)C for 4 minutes while the rate of cooling was altered. The force necessary to separate the tendon disks was then measured. The optimal temperature for tissue bonding (group I) was 62 degree(s)C (598 gm/in2). Stress values below 250 gm/in2 could be achieved without heat application and were considered non-welds. Group II showed that the faster the sample cools, the stronger the bond. Several conclusions can be postulated. The narrow temperature region necessary for tissue 'welding' strongly suggests that melting of type I collagen fibrils is involved. Bonding presumably occurs at 62 degree(s)C by allowing (alpha) -strands from the collagen super-helix molecule to form new, random connections. Group II results suggest that trans-incisional reannealing of unraveled helices does not play a role in tissue bonding. Rapid cooling allows less time for extended helix reformation; same-side a-helix reannealing may inhibit effective welds by reducing sites for trans-incisional visco-elastic bonding. Although the exact nature and optimization of thermal tissue 'welds' remains unclear, the behavior of collagen appears to play a central role.© (1991) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Differential Activation of CC Chemokine Receptors by AOP-RANTES (2000)

RANTES (regulated on activation normal T cell expressed) has been found at elevated levels in biological fluids from patients with a wide range of allergic and autoimmune diseases and is able to attract several subtypes of leukocytes including eosinophils and monocytes into inflamed tissue. Amino-terminal modifications of RANTES produce receptor antagonists which are candidates for blocking this cellular recruitment. Met-RANTES has been shown to modulate inflammation in vivo, while AOP-RANTES is a potent inhibitor of R5 human immunodeficiency virus type 1 (HIV-1) strains and has been shown to down-modulate CCR5 and prevent recycling of the receptor. We have studied the effect of AOP-RANTES in eosinophil activation and have found that it is able to efficiently elicit eosinophil effector functions through CCR3, as measured by the release of reactive oxygen species and calcium mobilization, whereas Met-RANTES is inactive in these assays. AOP-RANTES is found to inhibit CCR3-mediated HIV-1 infection with moderate potency, in contrast to its potent inhibition of CCR5-mediated HIV-1 infection. Furthermore, we have investigated the abilities of these modified proteins to down-modulate CCR1 and CCR3 from the surface of monocytes and eosinophils. We show here that AOP-RANTES is much less effective than RANTES in down-modulation of CCR1. Surprisingly, recycling of CCR1 was minimal after incubation with RANTES while there was complete recycling with AOP-RANTES. In the case of CCR3, no significant difference was found between RANTES and AOP-RANTES in down-modulation and recycling. It therefore appears that trafficking of RANTES receptors follows different patterns, which opens up potential new targets for therapeutic intervention.