gebhart/patrepeval huggingface dataset:
Rat forebrain neurogenesis and striatal neuron replacement after focal stroke (2002)

The persistence of neurogenesis in the forebrain subventricular zone (SVZ) of adult mammals suggests that the mature brain maintains the potential for neuronal replacement after injury. We examined whether focal ischemic injury in adult rat would increase SVZ neurogenesis and direct migration and neuronal differentiation of endogenous precursors in damaged regions. Focal stroke was induced in adult rats by 90-minute right middle cerebral artery occlusion (tMCAO). Cell proliferation and neurogenesis were assessed with bromodeoxyuridine (BrdU) labeling and immunostaining for cell type-specific markers. Brains examined 10-21 days after stroke showed markedly increased SVZ neurogenesis and chains of neuroblasts extending from the SVZ to the peri-infarct striatum. Many BrdU-labeled cells persisted in the striatum and cortex adjacent to infarcts, but at 35 days after tMCAO only BrdU-labeled cells in the neostriatum expressed neuronal markers. Newly generated cells in the injured neostriatum expressed markers of medium spiny neurons, which characterize most neostriatal neurons lost after tMCAO. These findings indicate that focal ischemic injury increases SVZ neurogenesis and directs neuroblast migration to sites of damage. Moreover, neuroblasts in the injured neostriatum appear to differentiate into a region-appropriate phenotype, which suggests that the mature brain is capable of replacing some neurons lost after ischemic injury.
Role of PPARγ in renoprotection in Type 2 diabetes: molecular mechanisms and therapeutic potential (2008)

DN (diabetic nephropathy) is a chronic disease characterized by proteinuria, glomerular hypertrophy, decreased glomerular filtration and renal fibrosis with loss of renal function. DN is the leading cause of ESRD (end-stage renal disease), accounting for millions of deaths worldwide. TZDs (thiazolidinediones) are synthetic ligands of PPARγ (peroxisome-proliferator-activated receptor γ), which is involved in many important physiological processes, including adipose differentiation, lipid and glucose metabolism, energy homoeostasis, cell proliferation, inflammation, reproduction and renoprotection. A large body of research over the past decade has revealed that, in addition to their insulin-sensitizing effects, TZDs play an important role in delaying and preventing the progression of chronic kidney disease in Type 2 diabetes. Although PPARγ activation by TZDs is in general considered beneficial for the amelioration of diabetic renal complications in Type 2 diabetes, the underlying mechanism(s) remains only partially characterized. In this review, we summarize and discuss recent findings regarding the renoprotective effects of PPARγ in Type 2 diabetes and the potential underlying mechanisms.
HLA-DR typing "at the DNA level": RFLPs and subtypes detected with a DR beta cDNA probe. (1988)

The HLA-DR beta gene, used as a hybridization probe, detects RFLPs that correlate with HLA-DR specificities. Using genomic DNA from more than 200 individuals, we have carried out a population study with a cDNA probe for the DR beta chain, which, under appropriate conditions, does not cross-hybridize with genes from other HLA-D subregions (e.g., DP and DQ). We first assessed the correspondence between serologically defined HLA-DR types and DNA patterns obtained after digestion with TaqI and found that DNA patterns allowed us to identify most specificities. Only two pairs of antigens are not distinguishable: with the DR beta probe alone we cannot distinguish DR3 from DRw6 or DR7 from DRw9. However, the correct assignment can always be made for the first pair by hybridizing the same digests with a DQ alpha or DQ beta probe. Thus DR typing from the DNA patterns is practical and accurate. We also looked for serologically undetectable subtypes. RFLPs revealed high-frequency subtypes for the specificities DR 2, 3, 5, w6, 7, and w9. Some of these are more accurately viewed as variant haplotypes, since the relevant variation is probably not at the DR beta locus that determines the serological specificities but rather at other closely linked and highly homologous DR beta loci such as DR beta-III. Nevertheless, the existence of variant haplotypes for so many specificities indicates a wealth of polymorphic variation beyond that detected serologically and provides more specific markers for studies of various diseases associated with HLA-DR specificities.
Colorimetric Gas Sensing with Enhanced Sensitivity (2016)

We present a colorimetric gas sensor system using folded sensing elements to obtain miniaturized, highly sensitive gas sensors. Our fabrication method offers the ease of transmission measurements and at the same time a substantial increase in sensitivity. The method is simple and cost-effective compared to waveguide-based solutions. Our colorimetric sensor was characterized using indicator dyes sensitive to ammonia (NH3) and carbon monoxide (CO). The sensing elements are placed between a LED and photodiodes for readout to realize a miniaturized sensor with low-cost components. First results show that by folding the sensing elements the sensitivity can be increased significantly. Ideas to optimize the number of sensing elements and sensor integration are discussed, as well as potential applications.
Prospective Study of Sudden Cardiac Death Among Women in the United States (2003)

These prospective data suggest that, as in men, coronary heart disease risk factors predict risk of SCD in women and that SCD is usually an arrhythmic death. Therefore, prevention of atherosclerosis or ventricular arrhythmias may reduce the incidence of SCD in women.
Antibody–Drug Conjugates for the Treatment of B-Cell Non-Hodgkin’s Lymphoma and Leukemia (2013)

Antibody-drug conjugates (ADCs) are a broad class of molecules comprising of a potent cytotoxic agent conjugated with a monoclonal antibody using a chemically stable linker. By selecting a monoclonal antibody directed against a tumor-specific or tumor-associated antigen, ADCs allow the targeted delivery of highly potent cytotoxic agents that result in unacceptable toxicity when administered as free agents. ADCs are currently being developed for the treatment of a wide variety of tumors. In this review, the current clinical and preclinical status of ADCs for the treatment of B-cell non-Hodgkin's lymphoma and B-cell leukemia will be discussed. ADCs have the potential to alter treatment paradigms for these diseases by providing both increased efficacy and improved safety and tolerability over current chemotherapy-based regimens.
RG7128 Alone or in Combination with Pegylated Interferon‐α2a and Ribavirin Prevents Hepatitis C Virus (HCV) Replication and Selection of Resistant Variants in HCV‐Infected Patients (2010)

The requirement for a predominant S282T mutant quasispecies, its low replication capacity, and the low-level resistance it confers probably contribute to the lack of RG7128 resistance observed in HCV-infected patients.
Direct Molecular Imaging ofLymnaea stagnalisNervous Tissue at Subcellular Spatial Resolution by Mass Spectrometry (2004)

The imaging capabilities of time-of-flight secondary ion mass spectrometry (ToF-SIMS) and MALDI-MS sample preparation methods were combined. We used this method, named matrix-enhanced (ME) SIMS, for direct molecular imaging of nervous tissue at micrometer spatial resolution. Cryosections of the cerebral ganglia of the freshwater snail Lymnaea stagnalis were placed on indium-tin-oxide (ITO)-coated conductive glass slides and covered with a thin layer of 2,5-dihydroxybenzoic acid by electrospray deposition. High-resolution molecular ion maps of cholesterol and the neuropeptide APGWamide were constructed. APGWamide was predominantly localized in the cluster of neurons that regulate male copulation behavior of Lymnaea. ME-SIMS imaging allows direct molecule-specific imaging from tissue sections without labeling and opens a complementary mass window (<2500 Da) to MALDI imaging mass spectrometry at an order of magnitude higher spatial resolution (<3 microm).
Optical and electronic properties of two dimensional graphitic silicon carbide (2012)

Optical and electronic properties of two dimensional few layers graphitic silicon carbide (GSiC), in particular monolayer and bilayer, are investigated by density functional theory and found different from that of graphene and silicene. Monolayer GSiC has direct bandgap while few layers exhibit indirect bandgap. The bandgap of monolayer GSiC can be tuned by an in-plane strain. Properties of bilayer GSiC are extremely sensitive to the interlayer distance. These predictions promise that monolayer GSiC could be a remarkable candidate for novel type of light-emitting diodes utilizing its unique optical properties distinct from graphene, silicene and few layers GSiC.
I2-Hydrosol-Seeded Growth of (I2)n-C-Codoped Meso/Nanoporous TiO2 for Visible Light-Driven Photocatalysis (2010)

We report a template-free process to fabricate (I2)n-C-codoped meso/nanoporous TiO2 nanocrystallites. I2 nanoparticles in I2-hydrosol were used as seeds to initial the nucleation of a precursory TiO2 shell formed by the hydrolysis of organotitanium molecules. The hybridized jumbles were further calcinated at different temperatures. The resulting (I2)n-C-codoped meso/nanoporous TiO2 structure was confirmed by transmission electron microscopy (TEM), X-ray diffraction (XRD), Brunauer−Emmett−Teller (BET) isotherm adsorption of N2. UV−visible diffuse reflectance spectroscopy (DRS) showed that (I2)n-C-codoped porous TiO2 samples have a strong absorption between 400−700 nm. The formation mechanism of (I2)n-C-codoped meso/nanoporous TiO2 spheres is discussed. Under visible light radiation, our samples exhibit superior ability in the photocatalytic degradation of methylene blue to that of the only C-doped TiO2 or to the commercial P25 TiO2 nanoparticles. The origin of the enhanced visible light−light driven photocatalytic degradation is attributed to the continuous states in the band gap of TiO2 introduced by I2 doping. Factors that contribute to the enhanced photocatalytic reaction are also studied, including the enhanced thermostability and conductivity of anatase TiO2 due to C doping, the location of I2 doping, as well as the morphology of the TiO2 structures.
Regularized Discrete Optimal Transport (2014)

This article introduces a generalization of the discrete optimal transport, with applications to color image manipulations. This new formulation includes a relaxation of the mass conservation constraint and a regularization term. These two features are crucial for image processing tasks where one must take into account families of multimodal histograms with large mass variation across modes. The corresponding relaxed and regularized transportation problem is the solution of a convex optimization problem. Depending on the regularization used, this minimization can be solved using standard linear programming methods or first order proximal splitting schemes. The resulting transportation plan can be used as a color transfer map, which is robust to mass variation across image color palettes. Furthermore, the regularization of the transport plan helps remove colorization artifacts due to noise amplification. We also extend this framework to compute the barycenter of distributions. The barycenter is the solution of an optimization problem, which is separately convex with respect to the barycenter and the transportation plans, but not jointly convex. A block coordinate descent scheme converges to a stationary point of the energy. We show that the resulting algorithm can be used for color normalization across several images. The relaxed and regularized barycenter defines a common color palette for those images. Applying color transfer toward this average palette performs a color normalization of the input images.
Neuropeptide Y infusion improves hemodynamics and survival in rat endotoxic shock (1993)

Neuropeptide Y (NPY), a sympathetic and platelet-derived vasoconstrictor, acts both directly and by potentiating adrenergic responsiveness and therefore may be beneficial in endotoxic shock, where suppressed vascular responsiveness to adrenergic agents is a key factor. This was studied in anesthetized rats. First, infusion of a nonhypotensive dose of endotoxin (lipopolysaccharide, LPS) markedly suppressed the pressor response to increasing doses of norepinephrine (NE), angiotensin II, and vasopressin but did not suppress the response to NPY. Second, in rats rendered hypotensive by intravenous LPS, continuous NE infusion (0.1-1.0 microgram.kg-1 x min-1 started 5 min after LPS for 1 h) did not alter hemodynamics. In contrast, 5 nmol.kg-1 x min-1 of NPY (equipotent to 0.1 microgram.kg-1 x min-1 of NE in normal rats) increased mean arterial pressure (MAP, from 64 to 114% of baseline), total peripheral resistance index (TPRI, from 64 to 154% of baseline), and left ventricular stroke work index (from 36 to 73% of baseline), without changing cardiac index (CI). Third, in a similar experimental protocol, pretreatment of the hypotensive rats with phentolamine blocked the pressor effect of NE infusion, but only partially attenuated the response to NPY. Finally, addition of low-dose NPY to NE infusion improved survival following a lethal dose of LPS compared with treatment with NE alone (P < 0.01). Thus, unlike other vasoconstrictors tested, NPY-mediated vasoconstriction is preserved during endotoxemia. The beneficial effect of NPY is mediated by increased TPRI without reduction in CI; both NPY receptor-mediated vasoconstriction and potentiation of adrenergic responsiveness may be involved.
Falls and Parkinsonʼs Disease (1989)

One hundred patients with Parkinson's disease (PD) and five patients with progressive supranuclear palsy were questioned about the frequency, circumstances, and consequences of falling. Parkinsonian symptoms were scored using the unified rating scale. Thirty-eight percent of parkinsonian patients fell, and 13% fell more than once a week. Broken bones (13%), hospitalization (18%), confinement to wheelchair (3%), and fear of walking occurred. Postural hypotension was uncommon and did not correlate to falling. Sensory loss, dementia, heart disease, and the use of antihypertensive medications were not related to falling. Falling did correlate with postural instability, bradykinesia, and rigidity but not with tremor. Falling was also related to age and duration of disease. The frequency of falling was correlated only to the severity of one parkinsonian symptom, postural instability. Progressive supranuclear palsy patients fell often and had marked postural instability. Factor analysis of parkinsonian characteristics yielded three groups, with tremor being an independent symptom. Frequent fallers and postural instability were not changed by dopaminergic therapy. Some fallers with gait difficulties and bradykinesia were improved with levodopa. Physical therapy was also of benefit to some patients. It is concluded that falling is a common problem in PD and may cause serious disability. Falling may be related to all the major motor signs except for tremor. Frequent falling is caused by postural instability, which is not reversible with dopaminergic therapy.
An in vitro DNA virus for in vitro protein evolution (2001)

In vitro virus is a molecular construct for in vitro protein evolution, which requires some mechanism to link phenotype to genotype. The first in vitro virus was realized by bonding a nascent protein with its coding mRNA via puromycin in in vitro translation. We report a new construct of in vitro DNA virus. The virion was a covalent cDNA-protein fusion, and virion formation did not require any modification of mRNA. Due to intactness of mRNA, this type of in vitro DNA virus will take the next step toward in vitro autonomous evolution, just like in vivo viral evolution in a cellstat.
Seroepidemiologic aspects of varicella zoster virus infections in an Israeli Jewish population. (1978)

Sera from 872 healthy subjects among the Jewish population of Israel were examined for antibodies to varicella zoster virus (VZV) by a simplified technique for the detection of immunofluorescent antibody to membrane antigen. The difference in the geometric mean titer of antibodies to the virus among the the different age groups was highly significant (P less than 0.0001). The highest titers were found in the five-to-seven-years and 21-to-30-years age groups. In 211 subjects, aged 17 to 40 years, the antibody titres were not influenced by sex or ethnic origin. The percentage of seronegative subjects (titer less than 2) was relatively high--between 18.7 and 32.9% in the 21-to-60-years age groups--and it was 19.5% in the population of childbearing age. The importance of screening for VZV immune status in pregnant women is emphasized.
Improved growth and thermal stability of Parylene films (1997)

Experimental results for the deposition of low dielectric constant Parylene-N and Parylene-F films are explained by a mechanism based on bulk phase diffusion reaction in the film. The deposition rate of Parylene-F decreases significantly as time increases and ultimately achieves steady state. Very favorable agreement with experiments at a substrate temperature of −10 °C is obtained for parylene-F with a rate constant of kf=5×10−5/s, and a diffusion coefficient Df=1.3×10−8 cm2/s. In contrast, the much higher rate constant at room temperature for Parylene-N films is kf=0.16/s and the predicted deposition rate is constant after a very small period of time (tss&amp;lt;4/kf=25 s). This prediction is confirmed by the experiments. The model predicts correctly that low deposition temperatures improve both the deposition rate and thermal stability of Parylene films. Our experiments confirm this prediction and one obtains both high growth rates and high molecular weight films at lower deposition temperatures. Furthermore, experiments show that the longer chains formed at low temperatures significantly improve the thermal stability of the films. The deposition rate also can be improved by using higher reactor pressures. However, the pressure that can be employed is limited to about 100 mTorr to maintain high quality films. At liquid nitrogen temperature (77 K), the deposition rate is three orders of magnitude larger than the film deposition rate at room temperature. The increased monomer concentration on the substrate due to higher condensation leads to this increased deposition rate.
Cleavage of supercoiled double‐stranded DNA by several ribosome‐inactivating proteins in vitro (1994)

Several ribosome-inactivating proteins (RIPs), such as ricin (including its A-chain), luffin, cinnamomin and camphorin, were found to express enzymatic activity to cleave supercoiled double-stranded DNA. In particular, alpha-sarcin, a RIP with a novel ribonuclease activity, was first proved to have this activity. They convert supercoiled DNA into a nicked circular conformation at low concentrations and further into a linear form at high concentrations: they have no effect on linear DNA. Although intact type II RIPs exhibited no RNA N-glucosidase activity, they were detected to cleave supercoiled DNA. Even if ricin A-chain was treated by boiling, its activity on supercoiled DNA was largely retained.
Assessment of the anti-viral effect of a short-term oral treatment of mice with live Saccharomyces cerevisiae cells. (1992)

For assessing the efficacy of antiviral treatments, influenza and herpes virus HSV-1 infections of varying degrees of severity have been produced. The infections proved to be reproducible with respect to both their course and death rate. These infections also exhibited a course slow enough to permit the assessment of treatments under conditions mimicking human infections and lent themselves to the choice of the best adapted strategy to treat an infection. A short-term oral treatment with live cells of S. cerevisiae was efficacious in protecting mice against mild influenza infection and partly but significantly against severe infection. On the other hand, it did not afford significant protection towards either mild or severe HSV-1 infections, but it significantly potentiated the effectiveness of the antiviral drug vidarabin. S. cerevisiae treatment induced the synthesis of IFN alpha but not that of TNF alpha.
Relationships between Transforming Growth Factor-β1, Myostatin, and Decorin (2007)

Recent studies have shown that myostatin, first identified as a negative regulator of skeletal muscle growth, may also be involved in the formation of fibrosis within skeletal muscle. In this study, we further explored the potential role of myostatin in skeletal muscle fibrosis, as well as its interaction with both transforming growth factor-beta1 and decorin. We discovered that myostatin stimulated fibroblast proliferation in vitro and induced its differentiation into myofibroblasts. We further found that transforming growth factor-beta1 stimulated myostatin expression, and conversely, myostatin stimulated transforming growth factor-beta1 secretion in C2C12 myoblasts. Decorin, a small leucine-rich proteoglycan, was found to neutralize the effects of myostatin in both fibroblasts and myoblasts. Moreover, decorin up-regulated the expression of follistatin, an antagonist of myostatin. The results of in vivo experiments showed that myostatin knock-out mice developed significantly less fibrosis and displayed better skeletal muscle regeneration when compared with wild-type mice at 2 and 4 weeks following gastrocnemius muscle laceration injury. In wild-type mice, we found that transforming growth factor-beta1 and myostatin co-localize in myofibers in the early stages of injury. Recombinant myostatin protein stimulated myofibers to express transforming growth factor-beta1 in skeletal muscles at early time points following injection. In summary, these findings define a fibrogenic property of myostatin and suggest the existence of co-regulatory relationships between transforming growth factor-beta1, myostatin, and decorin.
Nanoscale microcavity sensor for single particle detection (2007)

Recently we demonstrated a biosensor based on a two-dimensional photonic crystal microcavity for detection of proteins. We present a theoretical and experimental study of a modified structure for single particle detection. With an active sensing volume of approximately 0.15 microm(3), the device is capable of detecting approximately 1 fg of matter. Its performance is tested with latex spheres with sizes that fall in the size range of a variety of viruses.
Characterization of a cellobiose dehydrogenase from Humicola insolens (1998)

The major cellobiose dehydrogenase (oxidase) (CBDH) secreted by the soft-rot thermophilic fungus Humicola insolens during growth on cellulose has been isolated and purified. It was shown to be a haemoflavoprotein with a molecular weight of 92 kDa and a pI of 4.0, capable of oxidizing the anomeric carbon of cellobiose, soluble cellooligosaccharides, lactose, xylobiose and maltose. Possible electron acceptors are 2,6-dichlorophenol-indophenol (DCPIP), Methylene Blue, 3,5-di-t-butyl-1,2-benzoquinone, potassium ferricyanide, cytochrome c and molecular oxygen. The oxidation of the prosthetic groups by oxygen was monitored at 449 nm for the flavin group and at 562 nm for the haem group. The curves were very similar to those of the cellobiose dehydrogenase from Phanerochaete chrysosporium, suggesting a similar mechanism. The pH-optima for the oxidation varied remarkably depending on the electron acceptor. For the organic electron acceptors, the pH-optima ranged from pH 4 for Methylene Blue to pH 7 for DCPIP and the benzoquinone. In the case of the FeIII-containing electron acceptors, the enzyme displayed alkaline pH-optima, in contrast to the properties of cellobiose dehydrogenases from Phanerochaete chrysosporium and Myceliophthora (Sporotrichum) thermophila. The enzyme has optimal activity at 65 degrees C.