gebhart/patrepeval huggingface dataset:
Proteomic analysis of traumatic brain injury: the search for biomarkers (2008)

Although there are a number of causes of traumatic brain injury (TBI), the armed conflict in Iraq and Afghanistan has brought this disorder to the attention of the global community. A biomarker that would enable army medics to rapidly diagnose the severity of TBI on the battle-field would be a huge asset. Unfortunately, the study of TBI has not historically attracted the proteomic research community's interest as other disorders have, such as cancer. On the positive side, however, many of the analytical and technological challenges that were overcome in the development of biofluid proteomic methods are now being applied to the study of TBI. In this review, we discuss and highlight select examples of discovery-driven proteomic studies focused on finding effective biomarkers for TBI.
3D Descriptors for Object and Category Recognition: a Comparative Evaluation (2012)

Abstract — Often practitioners face the issue of choosing the most adequate 3D features for their problem. As with many other problems, there isn’t a “best ” feature to use. Nonetheless, we can gauge the relative accuracy of available features on common datasets. That is what we propose to do in this paper: we describe the existing feature extraction algorithms in a public available point cloud library and perform a comparative evaluation on 3D point clouds, investigation both the object and category recognition performance. The main conclusions are: increasing the number of keypoints improves recognition results at the expense of size and time; since there are big differences in terms of recognition performance, size and time requirements, the descriptor has to be matched to the desired task; one should use a descriptor that takes advantage of color; the SHOTCOLOR descriptor shows a good balance between recognition accuracy and time complexity. I.
Introduction and Overview (2008)

This chapter contains sections titled: Introduction What Soft Matter Is Characterization Techniques of Soft Matter Overview of the Book References
Chemically Functionalized Carbon Nanotubes as Substrates for Neuronal Growth (2004)

We report the use of chemically modified carbon nanotubes as a substrate for cultured neurons. The morphological features of neurons that directly reflect their potential capability in synaptic transmission are characterized. The chemical properties of carbon nanotubes are systematically varied by attaching different functional groups that confer known characteristics to the substrate. By manipulating the charge carried by functionalized carbon nanotubes we are able to control the outgrowth and branching pattern of neuronal processes.
Oxides grown on textured single-crystal silicon-dependence on process and application of EEPROMs (1990)

The electrical properties of oxides grown on textured single-crystal silicon (TSC oxides) are dependent on the process used to roughen or texture the single-crystal silicon surface. The effects of different processing steps on the I-V, C-V, charge trapping, interface trap generation, and breakdown characteristics of TSC oxides are examined. By choosing a particular set of processing steps, a TSC oxide can exhibit enhanced conduction and very good charge trapping and breakdown characteristics, which make it an interesting dielectric for EEPROM applications. Floating-gate EEPROMs fabricated using this TSC oxide demonstrate the feasibility of this new technology. Programming, cycling, and retention characteristics of this EEPROM are presented. In particular, the retention data of the TSC EEPROM show an improvement over those of EEPROMs using oxides grown on untextured single-crystal silicon.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Autoregulation and CO2 responses of cerebral blood flow in patients with acute severe head injury (1978)

✓ Regional cerebral blood flow (rCBF), cerebral intraventricular pressure (IVP), systemic arterial blood pressure, and cerebral ventricular fluid (CSF) lactate and pH were studied repeatedly in 23 patients during the acute phase of severe brain injury lasting from 3 to 21 days after the trauma. Cerebrovascular autoregulation was tested repeatedly by means of angiotensin infusion in 21 of the patients, and CO 2 response in 14 by means of passive hyperventilation. The pressure in the brain ventricles was measured continuously in all patients and kept below 45 mm Hg during the study. If the IVP increased more than 10 mm Hg during the angiotensin infusion (as in one case), the autoregulation test was considered contraindicated and the angiotensin infusion was discontinued. Dissociation between cerebrovascular autoregulation and CO 2 response was a common phenomenon. Typically, autoregulation appeared preserved in the most severely injured areas of the cerebral cortex when the patient was deeply comatose, but deteriorated concomitantly with recovery; by the time the patient became alert, the autoregulation was always impaired. The CO 2 response was impaired only in patients who were deeply comatose and had attacks of decerebrate rigidity; during recovery the CO 2 response became normal. Thus, preserved autoregulation associated with impaired CO 2 response indicated very severe brain damage, whereas impaired autoregulation associated with preserved CO 2 response suggested moderate or severe brain damage in recovery. These paradoxical observations raise the question whether the preserved autoregulation seen in severely injured brain tissue is a true autoregulation caused by an active vasoconstrictor response to an increase in blood pressure.
Definition of a Factor Va Binding Site in Factor Xa (2001)

We reported previously that residue 347 in activated fX (fXa) contributes to binding of the cofactor, factor Va (fVa) (Rudolph, A. E., Porche-Sorbet, R. and Miletich, J. P. (2000) Biochemistry 39, 2861-2867). Four additional residues that participate in fVa binding have now been identified by mutagenesis. All five resulting fX species, fX(R306A), fX(E310N), fX(R347N), fX(K351A), and fX(K414A), are activated and inhibited normally. However, the rate of inhibition by antithrombin III in the presence of submaximal concentrations of heparin is reduced for all the enzymes. In the absence of fVa, all of the enzymes bind and activate prothrombin similarly except fXa(E310N), which has a reduced apparent affinity ( approximately 3-fold) for prothrombin compared with wild type fXa (fXa(WT)). In the absence of phospholipid, fVa enhances the catalytic activity of fXa(WT) significantly, but the response of the variant enzymes was greatly diminished. On addition of 100 nm PC:PS (3:1) vesicles, fVa enhanced fXa(WT), fXa(R306A), and fXa(E310N) similarly, whereas fXa(R347N), fXa(K351A), and fXa(K414A) demonstrated near-normal catalytic activity but reduced apparent affinity for fVa under these conditions. All enzymes function similarly to fXa(WT) on activated platelets, which provide saturating fVa on an ideal surface. Loss of binding affinity for fVa as a result of the substitutions in residues Arg-347, Lys-351, and Lys-414 was verified by a competition binding assay. Thus, Arg-347, Lys-351, and Lys-414 are likely part of a core fVa binding site, whereas Arg-306 and Glu-310 serve a less critical role.
Multilocus Sequence Typing of Staphylococcus aureus with DNA Array Technology (2003)

A newly developed oligonucleotide array suited for multilocus sequence typing (MLST) of Staphylococcus aureus strains was analyzed with two strain collections in a two-center study. MLST allele identification for the first strain collection fully agreed with conventional strain typing. Analysis of strains from the second collection revealed that chip-defined MLST was concordant with conventional MLST. Array-mediated MLST data were reproducible, exchangeable, and epidemiologically concordant.
The effectiveness of anabolic agents in increasing rate of growth in farm animals; report on experiments in cattle. (1976)

In many countries anabolic agents are successfully used to increase the rate of growth of cattle. In the past widespread use was made of cheap synthetic estrogens such as diethylstilbestrol and hexestrol. However, new legislation in certain countries has restricted the use of synthetic estrogens. This has resulted in an intensive search by industry for alternative agents. On the one hand natural steroid hormones like estradiol, testosterone and progesterone were studied, while on the other hand products like an active compound of the resorcyclic acid lactones and the synthetic anabolic steroid trenbolone acetate were developed. Administration of anabolic agents to cattle is done in three ways. (1) The agent may be fed orally by incorporation into the concentrate feed or as a simple additive top dressing. If the agent is metabolised in the rumen, oral administration may still be possible by using coated materials which avoid rumen metabolism with subsequent absorption of the steroid from the small intestine. (2) The agent may be administered as a slow release implant, e.g. trenbolone acetate or various combined preparations of an androgen and estrogen. (3) Administration by repeated injection. This latter method is often impractical. Anabolic agents are normally administered to beef cattle or culled dairy cows during the last few months of the finishing period. Maximum weight gain performance in different types of cattle requires selection of the correct anabolic agent. Increased performance in female cattle is better when an androgenic steroid is administered. However, in intact males (bulls) best performance is only obtained when an estrogen, alone or in combination with an androgen, is administered. Castrate animals (steers) do best if a smaller amount of estrogen is combined with an androgen and administered, however there is evidence that androgen alone is as effective. In summary therefore, an additional response in growth of cattle may require the presence of an estrogen, as endogenous estrogen in the female and the exogenous form in the male. Only when this condition is met will administration of androgenic anabolic steroids result in maximum benefit, often improving the effect of estrogen given on its own. Anabolic agents have some beneficial effect on appetite. They may not affect the digestive processes of the alimentary system. They have a positive effect on nitrogen retention. The liver almost certainly has a central role in the regulation of nitrogen retention. Recent experiments suggest that urea entry rates in ruminants may be lowered, thus making available more nitrogen for protein synthesis. Muscle protein synthesis is altered with changes in carcass conformation. There are some changes in fat redistribution. How all these processes are integrated is not yet known. The possibility that anabolic agents establish a new hormonal status which is favourable to growth will be discussed...
Preweaning morbidity and mortality in the United States swine herd (1993)

In the first comprehensive, national effort to explore the scope and severity of swine disease and mortality, the USDA National Animal Health Monitoring System (NAHMS) conducted a National Swine Survey to gather data on preweaning morbidity and mortality in the United States swine herd. States were chosen on the basis of prior involvement in NAHMS programs and on the percentage of the nations hogs they contained, so that the states selected to particiPate represented 95% of hogs in the nation. Data collectors and producers were trained to enhance the likelihood that the data was valid. The most common cause of preweaning morbidity was scours, 42% of which occurred during the first 3 days postpartum. The most common causes of mortality were trauma (causing 43.2% of mortality), starvation (causing 20% of mortality), unknown causes (13.1%)and scours (10.8%). These common morbidity/mortality causes all suggest that management factors are responsible for the majority of preweaning morbidity/mortality in the United States swine herd.
Pharmacokinetics of Etilevodopa Compared to Levodopa in Patient's With Parkinson's Disease: An Open-label, Randomized, Crossover Study (2003)

"Dose failures" and "delayed on" phenomena following an intake of levodopa dose in patients with Parkinson's disease (PD) with motor fluctuations may be caused by stagnation of poorly soluble levodopa in the atonic stomach. Etilevodopa is a unique, highly soluble prodrug of levodopa. When ingested, etilevodopa is more readily dissolved in the stomach than levodopa. It passes unchanged through the stomach to the duodenum, where it is rapidly hydrolyzed by local esterases and rapidly absorbed as levodopa. To compare the pharmacokinetics of three different modes of etilevodopa/carbidopa administration with standard levodopa/carbidopa tablets in fluctuating PD patients, 29 patients with PD and response fluctuations were enrolled in an open-label, randomized, four-way crossover study of single doses of 4 treatments: swallowed etilevodopa/carbidopa tablets, etilevodopa/carbidopa tablets dissolved in water, etilevodopa oral solution with carbidopa tablets, and standard levodopa/carbidopa tablets. To measure the maximal concentration (Cmax), time to Cmax (tmax), and area under the curve (AUC) of plasma levodopa, etilevodopa, and carbidopa, blood samples were drawn before drug administration and at intervals up to 240 minutes thereafter. Plasma levodopa tmax was significantly shorter with all three modes of administration of etilevodopa (mean of about 30 minutes) than with levodopa treatment (mean of 54 minutes). During the first 45 minutes after drug ingestion, plasma levodopa AUC was significantly greater after etilevodopa administration than after levodopa administration. Levodopa AUC for 0 to 1 hour and 0 to 2 hours were also significantly greater following administration of etilevodopa/carbidopa swallowed tablets than following administration of levodopa/carbidopa tablets. Mean levodopa Cmax was in the range 2.3 to 2.7 microg/mL for all treatments. Levodopa Cmax was significantly greater following treatment with etilevodopa swallowed tablets than with levodopa tablets. Etilevodopa/carbidopa was well tolerated, with a safety profile comparable to that of levodopa/carbidopa. The shorter levodopa tmax observed with etilevodopa potentially translates to a shorter time to "on". Clinical trials with etilevodopa/carbidopa tablets should be carried out in PD patients with response fluctuations such as "delayed on" and "dose failures".
13C MR spectroscopy measurements of glutaminase activity in human hepatocellular carcinoma cells using hyperpolarized 13C‐labeled glutamine (2008)

Dynamic nuclear polarization (DNP) is an emerging technique for increasing the sensitivity of (13)C MR spectroscopy (MRS). [5-(13)C(1)]Glutamine was hyperpolarized using this technique by up to 5%, representing a 6000-fold increase in sensitivity. The conversion of hyperpolarized glutamine to glutamate by mitochondrial glutaminase was demonstrated using (13)C-MRS measurements in cultured human hepatoma cells (HepG2). These results represent the first step in developing an imaging technique for detecting glutamine metabolism in vivo. Furthermore, since glutamine utilization has been correlated with cell proliferation, the study suggests a new technique for detecting changes in tumor cell proliferation.
Antibody blockade of the Cripto CFC domain suppresses tumor cell growth in vivo (2003)

Cripto, a cell surface–associated protein belonging to the EGF-CFC family of growth factor–like molecules, is overexpressed in many human solid tumors, including 70–80% of breast and colon tumors, yet how it promotes cell transformation is unclear. During embryogenesis, Cripto complexes with Alk4 via its unique cysteine-rich CFC domain to facilitate signaling by the TGF-β ligand Nodal. We report, for the first time to our knowledge, that Cripto can directly bind to another TGF-β ligand, Activin B, and that Cripto overexpression blocks Activin B growth inhibition of breast cancer cells. This result suggests a novel mechanism for antagonizing Activin signaling that could promote tumorigenesis by deregulating growth homeostasis. We show that an anti–CFC domain antibody, A8.G3.5, both disrupts Cripto-Nodal signaling and reverses Cripto blockade of Activin B–induced growth suppression by blocking Cripto's association with either Alk4 or Activin B. In two xenograft models, testicular and colon cancer, A8.G3.5 inhibited tumor cell growth by up to 70%. Both Nodal and Activin B expression was found in the xenograft tumor, suggesting that either ligand could be promoting tumorigenesis. These data validate that functional blockade of Cripto inhibits tumor growth and highlight antibodies that block Cripto signaling mediated through its CFC domain as an important class of antibodies for further therapeutic development.
Arabinose-Derived Ketones as Catalysts for Asymmetric Epoxidation of Alkenes (2005)

[reaction: see text] Readily available arabinose-derived ketones, containing a tunable butane-2,3-diacetal as the steric blocker, displayed increasing enantioselectivity (up to 90% ee) with the size of the acetal alkyl group in catalytic asymmetric epoxidation of trans-disubstituted and trisubstituted alkenes. The stereochemical communication between our ketone catalysts and the alkene substrates is mainly due to steric effect, and electronic effect involving pi-pi interaction between phenyl groups of substrate and of catalyst did not appear to be operative in our system.
Stem cell bioprocessing: fundamentals and principles (2008)

In recent years, the potential of stem cell research for tissue engineering-based therapies and regenerative medicine clinical applications has become well established. In 2006, Chung pioneered the first entire organ transplant using adult stem cells and a scaffold for clinical evaluation. With this a new milestone was achieved, with seven patients with myelomeningocele receiving stem cell-derived bladder transplants resulting in substantial improvements in their quality of life. While a bladder is a relatively simple organ, the breakthrough highlights the incredible benefits that can be gained from the cross-disciplinary nature of tissue engineering and regenerative medicine (TERM) that encompasses stem cell research and stem cell bioprocessing. Unquestionably, the development of bioprocess technologies for the transfer of the current laboratory-based practice of stem cell tissue culture to the clinic as therapeutics necessitates the application of engineering principles and practices to achieve control, reproducibility, automation, validation and safety of the process and the product. The successful translation will require contributions from fundamental research (from developmental biology to the 'omics' technologies and advances in immunology) and from existing industrial practice (biologics), especially on automation, quality assurance and regulation. The timely development, integration and execution of various components will be critical-failures of the past (such as in the commercialization of skin equivalents) on marketing, pricing, production and advertising should not be repeated. This review aims to address the principles required for successful stem cell bioprocessing so that they can be applied deftly to clinical applications.
Two-Stage PCR Protocol Allowing Introduction of Multiple Mutations, Deletions and Insertions Using QuikChange TM Site-Directed Mutagenesis (1999)

We developed a two-stage procedure, based on the QuikChange Site-Directed Mutagenesis Protocol, that significantly expands its application to a variety of gene modification experiments. A pre-PCR, single-primer extension stage before the standard protocol allows the efficient introduction of not only point mutation but also multiple mutations and deletions and insertions to a sequence of interest.
Atrial Fibrillation Burden: Moving Beyond Atrial Fibrillation as a Binary Entity: A Scientific Statement From the American Heart Association (2018)

Our understanding of the risk factors and complications of atrial fibrillation (AF) is based mostly on studies that have evaluated AF in a binary fashion (present or absent) and have not investigated AF burden. This scientific statement discusses the published literature and knowledge gaps related to methods of defining and measuring AF burden, the relationship of AF burden to cardiovascular and neurological outcomes, and the effect of lifestyle and risk factor modification on AF burden. Many studies examine outcomes by AF burden classified by AF type (paroxysmal versus nonparoxysmal); however, quantitatively, AF burden can be defined by longest duration, number of AF episodes during a monitoring period, and the proportion of time an individual is in AF during a monitoring period (expressed as a percentage). Current guidelines make identical recommendations for anticoagulation regardless of AF pattern or burden; however, a review of recent evidence suggests that higher AF burden is associated with higher risk of stroke. It is unclear whether the risk increases continuously or whether a threshold exists; if a threshold exists, it has not been defined. Higher burden of AF is also associated with higher prevalence and incidence of heart failure and higher risk of mortality, but not necessarily lower quality of life. A structured and comprehensive risk factor management program targeting risk factors, weight loss, and maintenance of a healthy weight appears to be effective in reducing AF burden. Despite this growing understanding of AF burden, research is needed into validation of definitions and measures of AF burden, determination of the threshold of AF burden that results in an increased risk of stroke that warrants anticoagulation, and discovery of the mechanisms underlying the weak temporal correlations of AF and stroke. Moreover, developments in monitoring technologies will likely change the landscape of long-term AF monitoring and could allow better definition of the significance of changes in AF burden over time.
Herpes Simplex Virus as an in Situ Cancer Vaccine for the Induction of Specific Anti-Tumor Immunity (1999)

The success of cancer gene therapy is likely to require the targeting of multiple antitumor mechanisms. One strategy involves the use of attenuated, replication-competent virus vectors, such as herpes simplex virus type 1 (HSV-1) mutant G207, which is able to replicate in human tumor cells with resultant cell death and tumor growth inhibition, yet is nonpathogenic in normal tissue. In this study, we demonstrate that infection of established tumors with G207 also induces a highly specific systemic anti-tumor immune response. In a syngeneic, bilateral established subcutaneous tumor model, with mouse CT26 colorectal carcinoma cells in BALB/c mice or M3 melanoma cells in DBA/2 mice, unilateral intratumoral inoculation with G207 caused a significant reduction in the growth of both the inoculated and contralateral noninoculated tumors. This elicited anti-tumor response is dependent on viral infection of the tumor, as intradermal inoculation of G207 in BALB/c mice had no effect on CT26 tumor growth. Treatment of subcutaneous CT26 tumors by intratumoral inoculation of G207 induced a tumor-specific T cell response. CD8+ cytotoxic T lymphocyte (CTL) activity was generated that recognized a dominant "tumor-specific" major histocompatibility complex (MHC) class I-restricted epitope (AH1) from CT26 cells. In immune-competent animals, G207 is acting as an in situ tumor vaccine. Therefore, intratumoral G207 inoculation is able to inhibit tumor growth both by local cytotoxic viral replication in tumor cells and induction of a systemic anti-tumor immune response.
Beneficial Effects of Intracoronary Adenosine as an Adjunct to Primary Angioplasty in Acute Myocardial Infarction (2000)

Intracoronary adenosine administration is feasible and well tolerated in AMI. Adenosine adjunct to primary PTCA ameliorates flow, prevents the no-reflow phenomenon, improves ventricular function, and is associated with a more favorable clinical course.