gebhart/patrepeval huggingface dataset:
In vivo analysis of fluid transport in cystic fibrosis airway epithelia of bronchial xenografts (1996)

An in vivo human bronchial xenograft model system was used to simultaneously analyze electrolyte and fluid transport defects in fully differentiated human cystic fibrosis (CF) and non-CF proximal airways. CF airways demonstrated three discernible defects when compared with non-CF, including 1) a lack of adenosine 3',5'-cylic monophosphate (cAMP)-inducible Cl- secretion, 2) a fourfold higher basal fluid absorption rate, and 3) an altered regulation of fluid absorption in response to amiloride-stimulated changes in Na+ transport. A unique finding in this study demonstrated that treatment of epithelia with amiloride led to a greater than threefold decrease in the rate of fluid absorption in CF tissues as contrasted to a greater than threefold increase in the rate of fluid absorption in non-CF tissues. The removal of apical Na+ from amiloride-treated non-CF xenografts was capable of ablating this amiloride-induced increase in fluid absorption. In light of the recent interactions demonstrated between CF transmembrane conductance regulator (CFTR) and the rat epithelial, amiloride-sensitive Na+ channel, these findings implicate additional complexities between the Na+ conductance pathways and fluid transport in normal and CF proximal airways. Such findings suggest that CFTR may also regulate amiloride-insensitive Na+ channels.
An HTTP Flooding Detection Method Based on Browser Behavior (2006)

HTTP flooding is an attack that uses enormous useless packets to jam a Web server. In this paper, we use hidden semi-Markov models (HSMM) to describe Web-browsing patterns and detect HTTP flooding attacks. We first use a large number of legitimate request sequences to train an HSMM model and then use this legitimate model to check each incoming request sequence. Abnormal Web traffic whose likelihood falls into unreasonable range for the legitimate model would be classified as potential attack traffic and should be controlled with special actions such as filtering or limiting the traffic. Finally we validate our approach by testing the method with real data. The result shows that our method can detect the anomaly Web traffic effectively
Fractionation and identification of cellulases and other extracellular enzymes produced by Sporotrichum (Chrysosporium) thermophile during growth on cellulose or cellobiose (1983)

The extracellular enzyme proteins secreted by Sporotrichum (Chrysosporium) thermophile, ATCC 42 464, upon growth on cellulose or cellobiose, were separated by polyacrylamide gel electrophoresis and electrofocusing into different fractions which were then analyzed with respect to their enzymatic character to identify the cellulolytic enzymes. A positive reaction against carboxymethylcellulose azure (CMC azure) was taken as evidence for an endo-acting cellulase, whereas the criterion for the presence of an exo-cellulase was a negative reaction with CMC azure and a concomitant increase in reducing power upon action of any kind of cellulose. With this procedure, four main cellulolytic enzymes were detected: three endo-cellulases, named endo-cellulases I, II, and III (with corresponding isoelectric points 5.1, 4.2, 5.7), and an exo-cellulase (isoelectric point 4.7). With respect to their enzymatic action on amorphous cellulose, endo-cellulases I and III were isofunctional, releasing cellobiose and cellodextrins as hydrolytic products, whereas endo-cellulase II was found to produce additionally some glucose. Endo-cellulases I and III were also able to attack native (crystalline) cellulose like filter paper or Avicel, but endo-cellulase II could not and thus behaved as a true carboxymethylcellulase. The rate of formation of endo-cellulase I during growth was distinctly superior from that of the other cellulases so that the proportion of the activity due to endo-cellulase. I compared with that due to the others constantly increased during the culture.
Intraepithelial Lymphocytes Traffic to the Intestine and Enhance Resistance to Toxoplasma gondii Oral Infection (1999)

Toxoplasma gondii Ag-primed intraepithelial lymphocytes (IEL) from the mouse intestine have been shown to be protective against an lethal parasite challenge when adoptively transferred into recipient mice. In the present study, we observed that Ag-primed IEL traffic to the intestine of naive mice following i.v. administration. Primed and CD8beta+ IEL were the most efficient cells at homing to the host organ. In congenic mice, IEL migrated from intestine within several hours posttransfer. On Ag reexposure, the primed IEL return to the intestine where they enhance resistance as determined by reduction in the number of brain cysts. Treatment of recipient mice with anti-alpha4 and anti-alphaE Abs partially inhibited IEL intestinal homing. The Ab treatment dramatically impaired resistance to a subsequent oral infection. These finding indicate that lymphocyte homing is an important parameter in establishing long term immunity to recurrent infection with this parasite.
Wavelength selection and tuning by optical control in a two-segment erbium-doped fiber laser (1994)

A new method for controlling the wavelength of an Er/sup 3+/-doped fiber laser is proposed and demonstrated. Using two sections of dissimilar Er/sup 3+/-doped fiber and pumping them separately, switching among several distinct lasing wavelengths has been observed. Wavelength tuning over a range of 8 nm has also been achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clinical uses of intravenous immunoglobulin (2005)

There has been a rapid expansion in the use of intravenous immunoglobulin (IVIG) for an ever growing number of conditions. It is a product with an excellent safety record without the side effects of steroids or other immunosuppressive agents. There have been numerous recent advances in our understanding of the mechanisms of action of IVIG in many of the conditions for which it is being used, but there is still much to be learned. IVIG has had a major impact in neurology, haematology, immunology, rheumatology and dermatology. The limitations for IVIG are cost of the preparation itself and the logistical problems associated with its administration. Many of the side effects are managed easily by careful screening of the patient prior to treatment, premedication with analgesics and antihistamines and adjustment of infusion rate. It is likely, however, that side effects will be more frequent as the dose given increases and effects on plasma viscosity become greater [122]. It will be important to increase the evidence base for IVIG in many conditions to define its therapeutic role. In addition, there have been very few dose-ranging studies for hdIVIG and fewer still of which adjunctive agents (including biological agents such as rituximab and daclizumab) might offer the best therapeutic combinations.

Although not established, the use of IVIG is being studied in a range of conditions including heart failure, mycobacterial infection, adult respiratory distress syndrome, transplantation, fibrosis, connective tissue disease, encephalitis, epilepsy and even Alzheimer's disease. Should IVIG prove to be of efficacy in these settings it is likely to have major implications for drug budgets as many of the conditions are very common and place great strain on the world's supply of IVIG itself. Future studies will therefore need to address questions of efficacy, pharmacoeconomics, dose, adjunctive therapies and mechanism of action which may point the way to novel treatment strategies beyond IVIG. It is also clear, however, that controlled trials in many of the rare conditions may be very difficult to carry out and approaches such as prospective disease registries may be needed.
Tunable alexandrite lasers: Development and performance (1985)

Some major recent developments in alexandrite laser research are reviewed. Emphasis is placed on key material characteristics, and their relationship to laser performance. Alexandrite's favorable thermomechanical properties and high capacity for energy storage have led to laser performance levels that, in certain areas, exceed those of established solid-state laser sources. Here we review performance achievements for a variety of pulsed and CW laser configurations including single-mode, multimode, and mode-locked resonators, high-power amplifiers, and zig-zag slabs. In these configurations, operating performance levels have been demonstrated that are comparable to those of older, more familiar solid-state laser technologies. Alexandrite's broad tunability offers additional advantages. Together with nonlinear frequency conversion processes, alexandrite lasers provide high-brightness output over most of the UV, visible, and near IR.
Wireless Sensor Networks for integrated search and rescue efforts for disaster hit areas (2012)

The recent research and development in the domain of Wireless Sensor Networks (WSNs) have opened up tremendous opportunities and applications in many different scenarios. If we take into account the aftermaths of disaster, we certainly need to build up a mechanism to gather the data for the disaster hit area in which there is minimum delay and protocol we use should be energy efficient. This can be achieved by using wireless sensor network as they are energy efficient and can broadcast the data efficiently. The use of WSNs for search and rescue efforts is an evolving concept and numerous architectures have been studied and developed lately. This paper presents a conceptual design of a WSN based system aimed at aiding search and rescue missions in disaster hit area e.g. tsunami. People living in danger zone switch on their personal issued sensors after a warning is issued by relevant authorities. During and after disaster, this WSN is used to track and identify survivors, coordinate search efforts and assess on ground situation in real time.
Correction: Historical Mammal Extinction on Christmas Island (Indian Ocean) Correlates with Introduced Infectious Disease (2009)

It is now widely accepted that novel infectious disease can be a leading cause of serious population decline and even outright extinction in some invertebrate and vertebrate groups (e.g., amphibians). In the case of mammals, however, there are still no well-corroborated instances of such diseases having caused or significantly contributed to the complete collapse of species. A case in point is the extinction of the endemic Christmas Island rat (Rattus macleari): although it has been argued that its disappearance ca. AD 1900 may have been partly or wholly caused by a pathogenic trypanosome carried by fleas hosted on recently-introduced black rats (Rattus rattus), no decisive evidence for this scenario has ever been adduced. Using ancient DNA methods on samples from museum specimens of these rodents collected during the extinction window (AD 1888(AD -1908)), we were able to resolve unambiguously sequence evidence of murid trypanosomes in both endemic and invasive rats. Importantly, endemic rats collected prior to the introduction of black rats were devoid of trypanosome signal. Hybridization between endemic and black rats was also previously hypothesized, but we found no evidence of this in examined specimens, and conclude that hybridization cannot account for the disappearance of the endemic species. This is the first molecular evidence for a pathogen emerging in a na ve mammal species immediately prior to its final collapse.
Abnormal mannose-6-phosphate receptor trafficking impairs recombinant alpha-glucosidase uptake in Pompe disease fibroblasts (2008)

These results indicate a role for disrupted CI-MPR trafficking in the variable response to ERT in PD and have implications for ERT efficacy and optimization of treatment protocols.
<title>Surface femtochemistry by laser-excited hot electrons</title> (1994)

The paradigm of surface femtochemistry, laser induced desorption of molecules adsorbed on metal surfaces is considered, first from a `traditional' point of view and then from a contemporary one, suggested by experiments over the past five years. The key is laser excitation of substrate electrons followed by inelastic resonant scattering from the adsorbate. Theory is developed within the framework of Gaussian wavepacket dynamics.
Synthesis, Structure and Mechanism in Immunophilin Research (1994)

The ability to synthesize new molecular structures can greatly augment investigations of cellular systems. Synthetic chemistry coupled with structure determination is an especially powerful combination. These techniques have played a vital role in both the discovery and characterization of a family of intracellular receptors known as immunophilins. This review will attempt to highlight the synthetic and structural studies of immunophilin receptors that have been carried out in the Harvard and Cornell laboratories during the past several years.
Optogenetically enhanced axon regeneration: motor versus sensory neuron‐specific stimulation (2018)

Brief neuronal activation in injured peripheral nerves is both necessary and sufficient to enhance motor axon regeneration, and this effect is specific to the activated motoneurons. It is less clear whether sensory neurons respond in a similar manner to neuronal activation following peripheral axotomy. Further, it is unknown to what extent enhancement of axon regeneration with increased neuronal activity relies on a reflexive interaction within the spinal circuitry. We used mouse genetics and optical tools to evaluate the precision and selectivity of system-specific neuronal activation to enhance axon regeneration in a mixed nerve. We evaluated sensory and motor axon regeneration in two different mouse models expressing the light-sensitive cation channel, channelrhodopsin (ChR2). We selectively activated either sensory or motor axons using light stimulation combined with transection and repair of the sciatic nerve. Regardless of genotype, the number of ChR2-positive neurons whose axons had regenerated successfully was greater following system-specific optical treatment, with no effect on the number of ChR2-negative neurons (whether motor or sensory neurons). We conclude that acute system-specific neuronal activation is sufficient to enhance both motor and sensory axon regeneration. This regeneration-enhancing effect is likely cell autonomous.
Investigation of the role of lipids in the assembly of very low density lipoproteins in rabbit hepatocytes (1997)

Our aims were i) to determine which lipids colocalize with newly synthesized apolipoprotein (apo) B in the lumen of the rough endoplasmic reticulum (RER), and thus may play a role in the stabilization and/or translocation of this protein; and ii) to determine the intracellular sites of assembly of lipids into very low density lipoprotein (VLDL). In order to do this, we have developed a new method for the separation of ER-derived microsomes on self-generated gradients of iodixanol. Rabbit liver microsomes were resolved into two broad peaks, the lighter peak contained smooth vesicles and the heavier peak contained rough vesicles. Each peak was collected in a number of subfractions. A single gradient thus separates the initial events in the secretion process (RER fractions), from later events (smooth endoplasmic reticulum (SER) fractions). The microsomal fractions were separated into membranes and lumenal contents, and the mass of apoB and VLDL lipids determined by ELISA or high performance thin-layer chromatography, respectively. The biosynthetic relationships of apoB and lipids were investigated, in timed or chase experiments, by incubation of isolated rabbit hepatocytes with radiolabeled precursors of apoB or lipids, followed by isolation and analysis of the microsomal fractions. The results indicate that very small amounts of triacylglycerol, cholesterol, and cholesteryl ester co-localize with apoB into the lumen of the RER. The bulk of the VLDL lipids were in the lumen of the SER. However, some newly synthesized triacyl-glycerol, phospholipid, cholesterol, and cholesteryl ester were also transferred to the lumen of the RER and were chased into the SER lumen. Double-labeling experiments showed that cholesteryl ester produced from newly synthesized cholesterol (labeled with [3H]mevalonate and [14C]oleate) was almost exclusively present in the RER, while cholesteryl ester in the SER was labeled only with [14C]oleate. Thus, distinct intracellular lipid-pools may be involved at different stages in the assembly of VLDL.
Synthesis and Characterization of Photocrosslinkable Biodegradable Polymers Derived from 4‐Hydroxycinnamic Acid (2003)

Abstract A novel series of photocrosslinkable biodegradable polymers was prepared by a high‐temperature solution polycondensation from a dichloride of 4,4′‐(adipoyldioxy)dicinnamic acid (CAC) and alkane diols of various methylene lengths (HO(CH 2 ) n OH; n = 6–10) or poly(ethylene glycol)s (PEG) of various molecular weights $(\bar M = 200 - 8300)$ . The CAC was synthesized by the condensation of adipoyl chloride and 4‐hydroxycinnamic acid. The chemical structures and properties of these polymers were characterized by elemental analysis, ultraviolet‐visible spectroscopy (UV‐VIS), Fourier transform infrared spectroscopy (FT‐IR), 1 H NMR spectroscopy, differential scanning calorimertry (DSC), and thermogravimetry (TG). All polymers had a high molecular weight and good solubility in organic solvents. DSC showed that T m values of CAC n (134–180 °C) were much higher than those of CACE m (25–56 °C). The CACE200 degraded very rapidly in the buffer solutions (pH 7.2) of Ps. Cepacia or Rh. delemar lipase at 37 °C, while CAC n resisted the hydrolysis by these lipases during the test period. The ultraviolet light irradiation ( λ ≥ 280 nm) caused the photocrosslinking reaction by an intermolecular dimerization at ambient temperature without a photosensitizer, as examined by UV‐VIS, FT‐IR spectroscopy, and gel formation. The gels prepared from CACE m ( m ≈ 1 000) were swollen in water and showed characteristic properties of a hydrogel. The irradiation time and the molecular weight of PEGs controlled the degree of swelling of these hydrogels. The CACE8 300 gel irradiated for 20 min showed the largest degree of swelling of 10.5. Weight loss of a CACE200 film as a function of time in a phosphate buffer solution containing no lipase (□), Ps. cepacia lipase (•), or Rh. delemar lipase (○) at 37 °C. magnified image Weight loss of a CACE200 film as a function of time in a phosphate buffer solution containing no lipase (□), Ps. cepacia lipase (•), or Rh. delemar lipase (○) at 37 °C.
Control system architecture for a minimally invasive surgical robot. (2006)

As the field of surgical robotics continues to evolve, it is important to keep patient safety in mind. This paper describes a safety control architecture aimed at moving an experimental system in the direction of intrinsically safe operation. The system includes safety features such as: a small number of states, Programmable Logic Controller (PLC) state transition control, active enable, brakes, E-STOP, and a surgeon foot pedal.
Δ3,5-Δ2,4-Dienoyl-CoA Isomerase from Rat Liver (1998)

rECH1, a recently identified rat cDNA (FitzPatrick, D. R., Germain-Lee, E., and Valle, D. (1995) Genomics 27, 457-466) encodes a polypeptide belonging to the hydratase/isomerase superfamily. We modeled the structure of rECH1 based on rat mitochondrial 2-enoyl-CoA hydratase 1. The model predicts that rECH1p has the hydratase fold in the core domain and two domains for interaction with other subunits. When we incubated 3,5,8,11, 14-eicosapentaenoyl-CoA with purified rECH1p, the spectral data suggested a switching of the double bonds from the Delta3-Delta5 to the Delta2-Delta4 positions. This was confirmed by demonstrating that the product was a valid substrate for 2,4-dienoyl-CoA reductase. These results indicate that rECH1p is Delta3,5-Delta2,4-dienoyl-CoA isomerase. Subcellular fractionation and immunoelectron microscopy using antibodies to a synthetic polypeptide derived from the C terminus of rECH1p showed that rECH1p is located in the matrix of both mitochondria and peroxisomes in rat liver. Consistent with these observations, the 36,000-Da rECH1p has a potential N-terminal mitochondrial targeting signal as well as a C-terminal peroxisomal targeting signal type 1. Transport of the protein into the mitochondria with cleavage of the targeting signal results in a mature mitochondrial form with a molecular mass of 32,000 Da; transport to peroxisomes yields a protein of 36,000 Da.
Embryonic development of folate binding protein‐1 (Folbp1) knockout mice: Effects of the chemical form, dose, and timing of maternal folate supplementation (2004)

Inactivation of folate binding protein-1 (Folbp1) adversely impacts murine embryonic development, as nullizygous embryos (Folbp1(-/-)) die in utero. Administration of folinic acid (N5-formyl-tetrahydrofolate) to Folbp1-deficient dams before and throughout gestation rescues the majority of embryos from premature death; however, a portion of surviving embryos develop structural malformations, including neural tube defects. We examined whether maternal supplementation with L-N5-methyl-tetrahydrofolate (L-5M-THF) has superior protective effects on embryonic development of Folbp1(-/-) fetuses compared with L-N5-formyl-tetrahydrofolate (L-5F-THF). We also examined the critical period during gestation when folate supplementation is most beneficial to the developing Folbp1(-/-) embryos. Folbp1(-/-) pups presented with a range of malformations involving the neural tube, craniofacies, eyes, and abdominal wall. The frequencies of these malformations decreased with increasing folate dose, regardless of the form used. There was no additional benefit provided by L-5M-THF compared with L-5F-THF. Despite rescuing the phenotype in Folbp1(-/-) embryos, no significant elevation of Folbp1(-/-) maternal folate levels was observed with supplementation.
SAICAR Stimulates Pyruvate Kinase Isoform M2 and Promotes Cancer Cell Survival in Glucose-Limited Conditions (2012)

Pyruvate kinase isoform M2 (PKM2) plays an important role in the growth and metabolic reprogramming of cancer cells in stress conditions. Here, we report that SAICAR (succinylaminoimidazolecarboxamide ribose-5'-phosphate, an intermediate of the de novo purine nucleotide synthesis pathway) specifically stimulates PKM2. Upon glucose starvation, cellular SAICAR concentration increased in an oscillatory manner and stimulated PKM2 activity in cancer cells. Changes in SAICAR amounts in cancer cells altered cellular energy level, glucose uptake, and lactate production. The SAICAR-PKM2 interaction also promoted cancer cell survival in glucose-limited conditions. SAICAR accumulation was not observed in normal adult epithelial cells or lung fibroblasts, regardless of glucose conditions. This allosteric regulation may explain how cancer cells coordinate different metabolic pathways to optimize their growth in the nutrient-limited conditions commonly observed in the tumor microenvironment.