gebhart/patrepeval huggingface dataset:
The Tregs' world according to GARP (2009)

Naturally occurring CD4+CD25(high) regulatory T cells (nTreg) are essential for maintaining tolerance. FOXP3 has been established as a molecular marker of nTreg; however, FOXP3 cannot be used as a reliable marker for bona fide human nTreg since effector T cells also up-regulate FOXP3 expression upon activation. Despite the important function of nTreg, the underlying molecular mechanisms of nTreg-mediated suppression are far from defined. Previous studies have demonstrated that the TGF-beta latency-associated peptide (LAP) is expressed on the surface of nTreg, and that immunosuppression can be mediated by membrane TGF-beta; however, it remains unknown how LAP is bound to nTreg and what is the functional significance of its selective expression on activated nTreg. The nTreg's world may now change according to GARP, an orphan toll-like receptor composed of leucine-rich repeats. In this issue of the European Journal of Immunology, a study provides further demonstration that GARP is selectively expressed only in activated human nTreg and nTreg cell clones but not in activated effector T cells, confirming GARP as a bona fide nTreg marker. In addition, GARP binds directly to LAP; yet, GARP over-expression is insufficient to induce modification of latent TGF-beta into active TGF-beta further clarifying its role in nTreg-mediated suppression.
Molecular analysis of the sea anemone toxin Av3 reveals selectivity to insects and demonstrates the heterogeneity of receptor site-3 on voltage-gated Na+ channels (2007)

Av3 is a short peptide toxin from the sea anemone Anemonia viridis shown to be active on crustaceans and inactive on mammals. It inhibits inactivation of Na(v)s (voltage-gated Na+ channels) like the structurally dissimilar scorpion alpha-toxins and type I sea anemone toxins that bind to receptor site-3. To examine the potency and mode of interaction of Av3 with insect Na(v)s, we established a system for its expression, mutagenized it throughout, and analysed it in toxicity, binding and electrophysiological assays. The recombinant Av3 was found to be highly toxic to blowfly larvae (ED50=2.65+/-0.46 pmol/100 mg), to compete well with the site-3 toxin LqhalphaIT (from the scorpion Leiurus quinquestriatus) on binding to cockroach neuronal membranes (K(i)=21.4+/-7.1 nM), and to inhibit the inactivation of Drosophila melanogaster channel, DmNa(v)1, but not that of mammalian Na(v)s expressed in Xenopus oocytes. Moreover, like other site-3 toxins, the activity of Av3 was synergically enhanced by ligands of receptor site-4 (e.g. scorpion beta-toxins). The bioactive surface of Av3 was found to consist mainly of aromatic residues and did not resemble any of the bioactive surfaces of other site-3 toxins. These analyses have portrayed a toxin that might interact with receptor site-3 in a different fashion compared with other ligands of this site. This assumption was corroborated by a D1701R mutation in DmNa(v)1, which has been shown to abolish the activity of all other site-3 ligands, except Av3. All in all, the present study provides further evidence for the heterogeneity of receptor site-3, and raises Av3 as a unique model for design of selective anti-insect compounds.
Improving Acoustic Models by Watching Television (1998)

Obtaining sufficient labelled training data is a persistent difficulty for speech recognition research. Although well transcribed data is expensive to produce, there is a constant stream of challenging speech data and poor transcription broadcast as closed-captioned television. We describe a reliable unsupervised method for identifying accurately transcribed sections of these broadcasts, and show how these segments can be used to train a recognition system. Starting from acoustic models trained on the Wall Street Journal database, a single iteration of our training method reduced the word error rate on an independent broadcast television news test set from 62.2% to 59.5%.
Enhancement of Amino Acid Detection and Quantification by Electrospray Ionization Mass Spectrometry (2006)

A new strategy for amino acid analysis is reported involving derivatization with an N-hydroxysuccinimide ester of N-alkylnicotinic acid (Cn-NA-NHS) followed by reversed-phase chromatography and electrospray ionization mass spectrometry (RPC-MS). Detection sensitivity increased as the N-alkyl chain length of the nicotinic acid derivatizing agent was increased from 1 to 4. N-Acylation of amino acids with the Cn-NA-NHS reagents in water produced a stable product in roughly 1 min using a 4-fold molar excess of derivatizing agent in 0.1 M sodium borate buffer at pH values ranging from 8.5 to 10. Some O-acylation of tyrosine was also observed, but the product hydrolyzed within a few minutes at pH 10. The cystine product also degraded slowly over the course of a few days from reduction of the disulfide bond to form cysteine. The retention time of Cn-NA derivatized amino acids was lengthened in reversed-phase chromatography to the extent that polar amino acids were retained beyond the solvent peak, particularly in the cases of the C3-NA and C4-NA derivatives. Complete resolution of 18 amino acids was achieved in 28 min using the C4-NA-NHS reagent. Compared to N-acylation with benzoic acid, derivatization with C4-NA-NHS increased MS detection sensitivity 6-80-fold. This was attributed to the surfactant properties of the Cn-NA-NHS reagents. The quaternary amine increased the charge on amino acid conjugates while the presence of an adjacent alkyl chain further increased ionization efficiency by apparently enhancing amino acid migration to the surface of electrospray droplets. Further modification of the Cn-NA-NHS reagents with deuterium was used to prepare coded sets of derivatizing agents. These coding agents were used to differentially code samples and after mixing carry out comparative concentration measurements between samples using extracted ion chromatograms to estimate relative peak areas of derivatized amino acids.
Immunomodulatory and Antimicrobial Efficacy of Intravenous Immunoglobulin in Bone Marrow Transplantation (1990)

Passive immunotherapy with intravenous immunoglobulin decreases the risk of acute GVHD, associated interstitial pneumonia, and infections after bone marrow transplantation.
Recent advances in digital holography [Invited] (2014)

This article presents an overview of recent advances in the field of digital holography, ranging from holographic techniques designed to increase the resolution of microscopic images, holographic imaging using incoherent illumination, phase retrieval with incoherent illumination, imaging of occluded objects, and the holographic recording of depth-extended objects using a frequency-comb laser, to the design of an infrastructure for remote laboratories for digital-holographic microscopy and metrology. The paper refers to current trends in digital holography and explains them using new results that were recently achieved at the Institute for Applied Optics of the University Stuttgart.
Analysis of recombinant adeno-associated virus packaging and requirements for rep and cap gene products (1997)

Adeno-associated virus (AAV) is a human parvovirus currently being developed as a vector for gene therapy applications. Because the gene transfer vector commonly retains only the AAV terminal repeats, propagation of recombinant AAV (rAAV) requires that the viral replication (Rep) and capsid (Cap) proteins be supplied in trans. In an effort to optimize the production of these vectors, a panel of helper plasmids was constructed to determine if expression of the rep and/or cap genes is a limiting factor for rAAV packaging. Expression of the Rep and Cap proteins was increased by replacing the endogenous AAV promoters, p5 and p40, with the Rous sarcoma virus (RSV) long terminal repeat (LTR) and the cytomegalovirus immediate-early promoter, respectively. Increased synthesis of the Cap proteins resulted in an approximately 10-fold increase in the yield of rAAV, indicating that production of capsid proteins is one limiting factor for rAAV packaging. Expression of the rep gene from the RSV LTR not only failed to increase the yield of rAAV but also prevented activation of p40 transcription with adenovirus infection, resulting in a reduced level of capsid protein synthesis.
DNA Ligase: Structure, Mechanism, and Function (1974)

DNA ligase of E. coli is a polypeptide of molecular weight 75,000. The comparable T4-induced enzyme is somewhat smaller (63,000 to 68,000). Both enzymes catalyze the synthesis of phosphodiester bonds between adjacent 5'-phosphoryl and 3'-hydroxyl groups in nicked duplex DNA, coupled to the cleavage of the pyrophosphate bond of DPN (E. coli) or ATP (T4). Phosphodiester bond synthesis catalyzed by both enzymes occurs in a series of these discrete steps and involves the participation of two covalent intermediates (Fig. 1). A steady state kinetic analysis of the reaction-catalyzed E. coli ligase supports this mechanism, and further demonstrates that enzyme-adenylate and DNA-adenylate are kinetically significant intermediates on the direct path of phosphodiester bond synthesis. A strain of E. coli with a mutation in the structural gene for DNA ligase which results in the synthesis of an abnormally thermolabile enzyme is inviable at 42 degrees C. Although able to grow at 30 degrees C, the mutant is still defective at this temperature in its ability to repair damage to its DNA caused by ultraviolet irradiation and by alkylating agents. At 42 degrees C, all the newly replicated DNA is in the form of short 10S "Okazaki fragments," an indication that the reason for the mutant's failure to survive under these conditions is its inability to sustain the ligation step that is essential for the discontinuous synthesis of the E. coli chromosome. DNA ligase is therefore an essential enzyme required for normal DNA replication and repair in E. coli. Purified DNA ligases have proved to be useful reagents in the construction in vitro of recombinant DNA molecules.
Analysis of the rotting process of rice straw-calcium cyanamide mixture by physical fractionation (1975)

Abstract The rotting process of a rice straw-calcium cyanamide mixture (rice straw compost) at 50°C, was studied by physical fractionation methods. The compost was divided into six fractions using a combination of methods which included the use of different sizes of sieves, sedimentation, and centrifugation. The six fractions obtained are Fl (1.0 mm), F2 (1.0–0.25 mm), F3 (0.25–0.043 mm), F4 (sedimented at 4°C), F5 (sedimented by centrifugation at 104 × g for 10 min), and F6 (supernatant). The results obtained are summarized as follows: 1. With the progress of rotting, rice straw became finely divided, and about 80% of dry matter consisted of fractions F4, FS, and F6 within 10 weeks. The distribution of size fractions remained nearly constant afterwards. 2. The same trends were observed for the fractional distribution of carbon and nitrogen per pot. They were distributed in the order of F6>F5>F4 and F5>F6>F4, respectively. 3. Eighty-five to 90% of the total nitrogen was concentrated in fractions F4-6. 4. C/N ratio of each fraction was almost constant after 5 weeks incubation, except for Fl, and the values decreased with a decrease in size. 5. Ash content of each size fraction was nearly unchanged after 10 weeks, Ash was concentrated in fraction F4. 6. The fractions obtained by physical fractionation of rice straw compost were tentatively divided into three major groups: I. Fractions Fl-3 consist of coarse plant tissues which became dull yellowish brown to grayish yellow brown. II. Fractions F4 and F5 consist of fine grayish yellow brown plant tissues, microbial cells, and their debris. III. Fraction F6 consists of humic substances.
mRNA‐Mediated Gene Delivery Into Human Progenitor Cells Promotes Highly Efficient Protein Expression (2007)

Gene transfer into human CD34+ haematopoietic progenitor cells (HPC) and multi-potent mesenchymal stromal cells (MSC) is an essential tool for numerous in vitro and in vivo applications including therapeutic strategies, such as tissue engineering and gene therapy. Virus based methods may be efficient, but bear risks like tumorigenesis and activation of immune responses. A safer alternative is non-viral gene transfer, which is considered to be less efficient and accomplished with high cell toxicity. The truncated low affinity nerve growth factor receptor (ALNGFR) is a marker gene approved for human in vivo application. Human CD34+ HPC and human MSC were transfected with in vitro-transcribed mRNA for DeltaLNGFR using the method of nucleofection. Transfection efficiency and cell viability were compared to plasmid-based nucleofection. Protein expression was assessed using flow cytometry over a time period of 10 days. Nucleofection of CD34+ HPC and MSC with mRNA resulted in significantly higher transfection efficiencies compared to plasmid transfection. Cell differentiation assays were performed after selecting DeltaLNGFR positive cells using a fluorescent activating cell sorter. Neither cell differentiation of MSC into chondrocytes, adipocytes and osteoblasts, nor differentiation of HPC into burst forming unit erythroid (BFU-E) colony forming unit-granulocyte, erythrocyte, macrophage and megakaryocyte (CFU-GEMM), and CFU-granulocyte-macrophage (GM) was reduced. mRNA based nucleofection is a powerful, highly efficient and non-toxic approach for transient labelling of human progenitor cells or, via transfection of selective proteins, for transient manipulation of stem cell function. It may be useful to transiently manipulate stem cell characteristics and thus combine principles of gene therapy and tissue engineering.
Antitumor Activity of ZSTK474, a New Phosphatidylinositol 3-Kinase Inhibitor (2006)

ZSTK474 is a new PI3K inhibitor with strong antitumor activity against human cancer xenografts without toxic effects in critical organs. ZSTK474 merits further investigation as an anticancer drug.
NSAIDs and Cancer Prevention: Targets Downstream of COX-2 (2006)

Preclinical and clinical studies have clearly shown a benefit of nonsteroidal anti-inflammatory drug (NSAID) use in reducing cancer risk. However, the adverse gastrointestinal and cardiovascular side effects associated with NSAIDs and COX-2 selective inhibitors (coxibs) have provoked more scrutiny of the precise role of specific downstream mediators in the prostaglandin (PG) signaling cascade. NSAIDs and coxibs inhibit PG biosynthesis. One of the PGs produced at high levels in the tumor microenvironment is PGE(2), which is thought to play a major role in cancer progression. Thus, a better understanding of PGE(2) signaling could enable identification of novel and safer therapeutic targets downstream of the cyclooxygenase enzymes. We review the emerging molecular mechanisms by which COX-2-derived PGE(2) is involved in cancer progression and delineate potential opportunities for development of novel pharmacologic approaches utilizing this pathway.
Antiallergic activity of a disaccharide isolated from Sanguisorba ofﬁcinalis (2004)

The antiallergic activity of the natural disaccharide, 5-O-alpha-D-(3-C-hydroxymethyl)lyxofuranosyl-beta-D-(2-C-hydroxymethyl)arabinofuranose was evaluated using both in vivo and in vitro experimental models. Intravenously administered compound inhibited the passive cutaneous anaphylaxis response in rats in a dose-dependent manner (ED(50) = 9.6 mg/kg). The compound inhibited histamine release evoked by both compound 48/80 and calcium ionophore A23187 in rat peritoneal mast cells indicating that mast cell stabilization is the major mechanism of action for its antiallergic activity. In passively sensitized isolated guinea-pig hearts, an in vitro anaphylaxis model in which histamine release plays a key role for functional deterioration, the compound markedly diminished both coronary flow reduction and histamine release on challenge to the antigen. These data demonstrate that this antiallergic natural disaccharide exerts its effect via inhibition of mast cell mediator release.
Long-Term Follow-Up of Patients With Mild Coronary Artery Disease and Endothelial Dysfunction (2000)

Severe endothelial dysfunction in the absence of obstructive coronary artery disease is associated with increased cardiac events. This study supports the concept that coronary endothelial dysfunction may play a role in the progression of coronary atherosclerosis.
CD41 expression marks myeloid-biased adult hematopoietic stem cells and increases with age (2013)

The hematopoietic stem cell (HSC) compartment is heterogeneous, yet our understanding of the identities of different HSC subtypes is limited. Here we show that platelet integrin CD41 (αIIb), currently thought to only transiently mark fetal HSCs, is expressed on an adult HSC subtype that accumulates with age. CD41+ HSCs were largely quiescent and exhibited myeloerythroid and megakaryocyte gene priming, governed by Gata1, whereas CD41- HSCs were more proliferative and exhibited lymphoid gene priming. When isolated without the use of blocking antibodies, CD41+ HSCs possessed long-term repopulation capacity on serial transplantations and showed a marked myeloid bias compared with CD41- HSCs, which yielded a more lymphoid-biased progeny. CD41-knockout (KO) mice displayed multilineage hematopoietic defects coupled with decreased quiescence and survival of HSCs, suggesting that CD41 is functionally relevant for HSC maintenance and hematopoietic homeostasis. Transplantation experiments indicated that CD41-KO-associated defects are long-term transplantable, HSC-derived and, in part, mediated through the loss of platelet mass leading to decreases in HSC exposure to important platelet released cytokines, such as transforming growth factor β1. In summary, our data provide a novel marker to identify a myeloid-biased HSC subtype that becomes prevalent with age and highlights the dogma of HSC regulation by their progeny.
Effect of Pelvic Tilt on Acetabular Retroversion: A Study of Pelves From Cadavers (2003)

Pelvic inclination is difficult to control on a standard radiograph of the pelvis and has a direct influence on the appearance of acetabular version. By defining the normal range of the distance between the symphysis and the sacrococcygeal joint on 86 standard anteroposterior radiographs of pelves a technique was developed to evaluate pelvic inclination. A statistically significant correlation between this distance and pelvic inclination was shown in four cadaver pelves. Acetabular retroversion signs (cross-over, posterior wall signs) were evaluated on normal pelves from cadavers (two females, two males) after mounting on a holding device and wire marking of the acetabular rims. Radiographs were taken 3 degrees stepwise through the range of 9 degrees inclination to 12 degrees reclination. At the neutral position, two acetabula appeared with both positive retroversion signs compared with none at 6 degrees reclination. At 9 degrees pelvic inclination all acetabula had both signs. Retroversion signs were significantly more pronounced and found at lower pelvic tilt angles in the pelves from males than from females. Evaluation of pelvic inclination will help to decrease measurement errors in assessment of acetabular orientation and femoral head coverage. This will be valuable in preoperative planning of reorientation procedures.
Production of Hepatocyte Growth Factor Is Increased in Chronic Renal Failure (1997)

Hepatocyte growth factor (HGF) facilitates recovery from tissue injuries. We previously reported that serum HGF levels were elevated in chronic renal failure (CRF) patients. In the present study Western blot analysis of CRF patients' sera showed the majority of their serum HGF was a single-chain precursor molecule. In CRF rats developed by 5/6 nephrectomy or high adenine diet, both HGF mRNA expression levels and tissue HGF concentrations were increased in liver and spleen. The results suggest that HGF production increases in CRF, which may be a response to chronic progressive renal injuries in an endocrine manner.
Car that Knows Before You Do: Anticipating Maneuvers via Learning Temporal Driving Models (2015)

Advanced Driver Assistance Systems (ADAS) have made driving safer over the last decade. They prepare vehicles for unsafe road conditions and alert drivers if they perform a dangerous maneuver. However, many accidents are unavoidable because by the time drivers are alerted, it is already too late. Anticipating maneuvers beforehand can alert drivers before they perform the maneuver and also give ADAS more time to avoid or prepare for the danger. In this work we anticipate driving maneuvers a few seconds before they occur. For this purpose we equip a car with cameras and a computing device to capture the driving context from both inside and outside of the car. We propose an Autoregressive Input-Output HMM to model the contextual information alongwith the maneuvers. We evaluate our approach on a diverse data set with 1180 miles of natural freeway and city driving and show that we can anticipate maneuvers 3.5 seconds before they occur with over 80% F1-score in real-time.
FACTS: flexible alternating current transmission systems (2005)

Increased demands on transmission, absence of long-term planning and the need to provide open access to generating companies and customers have created tendencies toward less security and reduced quality of supply. The FACTS technology is essential to alleviate some but not all of these difficulties. The FACTS technology opens up new opportunities for controlling power and enhancing the usable capacity of present, as well as new and upgraded, lines. The possibility that current and therefore power through a line can be controlled enables a large potential of increasing the capacity of existing lines. These opportunities arise through the ability of FACTS controllers to control the interrelated parameters that govern the operation of transmission systems including series impedance, shunt impedance, current, voltage, phase angle and the damping of oscillations. This report is an overview of the existing FACTS devices. It is mainly a summary of [1], [2], [3] where more extensive elaborations on FACTS devices can be found. The IEEE definition to these devices are given in italic in the corresponding sections.
Treatment of multiple sclerosis with the pregnancy hormone estriol (2002)

Multiple sclerosis patients who become pregnant experience a significant decrease in relapses that may be mediated by a shift in immune responses from T helper 1 to T helper 2. Animal models of multiple sclerosis have shown that the pregnancy hormone, estriol, can ameliorate disease and can cause an immune shift. We treated nonpregnant female multiple sclerosis patients with the pregnancy hormone estriol in an attempt to recapitulate the beneficial effect of pregnancy. As compared with pretreatment baseline, relapsing remitting patients treated with oral estriol (8 mg/day) demonstrated significant decreases in delayed type hypersensitivity responses to tetanus, interferon-gamma levels in peripheral blood mononuclear cells, and gadolinium enhancing lesion numbers and volumes on monthly cerebral magnetic resonance images. When estriol treatment was stopped, enhancing lesions increased to pretreatment levels. When estriol treatment was reinstituted, enhancing lesions again were significantly decreased. Based on these results, a larger, placebo-controlled trial of estriol is warranted in women with relapsing remitting multiple sclerosis. This novel treatment strategy of using pregnancy doses of estriol in multiple sclerosis has relevance to other autoimmune diseases that also improve during pregnancy.