gebhart/patrepeval huggingface dataset:
PORs: Proofs of Retrievability for Large Files (2007)

Abstract. In this paper, we define and explore proofs of retrievability (PORs). A POR scheme enables an archive or back-up service (prover) to produce a concise proof that a user (verifier) can retrieve a target file F, that is, that the archive retains and reliably transmits file data sufficient for the user to recover F in its entirety. A POR may be viewed as a kind of cryptographic proof of knowledge (POK), but one specially designed to handle a large file (or bitstring) F. We explore POR protocols here in which the communication costs, number of memory accesses for the prover, and storage requirements of the user (verifier) are small parameters essentially independent of the length of F. In addition to proposing new, practical POR constructions, we explore implementation considerations and optimizations that bear on previously explored, related schemes. In a POR, unlike a POK, neither the prover nor the verifier need actually have knowledge of F. PORs give rise to a new and unusual security definition whose formulation is another contribution of our work. We view PORs as an important tool for semi-trusted online archives. Existing cryptographic techniques help users ensure the privacy and integrity of files they retrieve. It is also natural, however, for users to want to verify that archives do not delete or modify files prior to retrieval. The goal of a POR is to accomplish these checks without users having to download the files themselves. A POR can also provide quality-of-service guarantees, i.e., show that a file is retrievable within a certain time bound. Key words: storage systems, storage security, proofs of retrievability, proofs of knowledge 1
Chemotherapy-Induced Peripheral Neuropathy (2019)

Chemotherapy-Induced Peripheral NeuropathyPeripheral neuropathy refers to symptoms arising from damage to peripheral nerves.These nerves carry sensation, control movements of the arms and legs, and control the bladder and bowel.Chemotherapy and other drugs used to treat cancer can cause peripheral neuropathy.This is termed chemotherapy-induced peripheral neuropathy (or CIPN).
Early Assembly Step of a Retroviral Envelope Glycoprotein: Analysis Using a Dominant Negative Assay (1999)

As for most integral membrane proteins, the intracellular transport of retroviral envelope glycoproteins depends on proper folding and oligomeric assembly in the ER. In this study, we considered the hypothesis that a panel of 22 transport-defective mutants of the human T cell leukemia virus type 1 envelope glycoprotein might be defective in ER assembly. Upon cell cotransfection with wild-type envelope, however, the vast majority of these transport-defective mutants (21 of 22) exerted a specific trans-dominant negative effect. This effect was due to random dimerization of the mutated and wild-type glycoproteins that prevented the intracellular transport of the latter. This unexpected result suggests that association of glycoprotein monomers precedes the completion of folding. The only mutation that impaired this early assembly was located at the NH2 terminus of the protein. COOH-terminally truncated, soluble forms of the glycoprotein were also trans-dominant negative provided that their NH2 terminus was intact. The leucine zipper-like domain, although involved in oligomerization of the envelope glycoproteins at the cell surface, did not contribute to their intracellular assembly. We propose that, at a step subsequent to translation, but preceding complete folding of the monomers, glycoproteins assemble via their NH2-terminal domains, which, in turn, permits their cooperative folding.
Adoptive cancer immunotherapy using genetically engineered designer T-cells: First steps into the clinic. (2010)

The treatment of patients with cancer using passive vaccination with antibodies has been demonstrated to be a promising option, particularly for 'soft tumors', most likely because of their greater accessibility compared with bulky solid tumors. While effector T-cells are efficient in the rejection of large organs and foreign tissues, the wide application of tumor-specific T-cells for cancer therapy has been limited by the inherent restriction of T-cell recognition to self antigens, and the difficulty in obtaining sufficient numbers of such cells with defined specificity. Advances in gene transfer and cell therapy have enabled the genetic modification of T-cells by the ectopic expression of predefined, specific receptor genes that redirect such 'designer cells' to any target of interest. This review discusses two approaches to applying redirected T-cells for adoptive cancer immunotherapy: the 'T-body' approach, which employs chimeric receptors with tumor-specific antibody-derived specificity, and the use of transgenes encoding tumor-specific T-cell receptors. Particular emphasis is placed on recent attempts using these approaches in the treatment of patients with cancer.
Involvement of small RNAs and role of the qde genes in the gene silencing pathway in Neurospora (2002)

Small RNA molecules have been found to be specifically associated with posttranscriptional gene silencing (PTGS) in both plants and animals. Here, we find that small sense and antisense RNAs are also involved in PTGS in Neurospora crassa. The accumulation of these RNA molecules depends on the presence of functional qde-1 and qde-3 genes previously shown to be essential for gene silencing, but does not depend on a functional qde-2, indicating that this gene is involved in a downstream step of the gene silencing pathway. Supporting this idea, a purified QDE2 protein complex was found to contain small RNA molecules, suggesting that QDE2 could be part of a small RNA-directed ribonuclease complex involved in sequence-specific mRNA degradation.
On the 5q- deletion: clinical and cytogenetic observations in ten patients and review of the literature (1981)

Clinical and cytogenetic findings in 10 patients with deletions of the long arm of chromosomes 5 (5q-) are reported. Five cases had refractory anemia, the preleukemic syndrome, or refractory anemia with an excess of blasts; in all but one, the 5q- was the single initial abnormality. Three patients had overt leukemia; in all, the 5q- was accompanied by additional anomalies. Two patients had a myeloproliferative disorder. In one of these, a case of polycythemia vera, the 5q- appeared secondarily to other karyotypic abnormalities and concomitantly with transformation into a “spent phase.” The deletions were interstitial in most cases, and even if the size of the deletion varied, the region q15- q31 was lost in all cases except 2. Bone marrow from all cases except one showed a marked increase in the number of megakaryocytes. A survey of the literature yielded a total of 69 evaluable patients with 5q- deletions, including the present series. The 5q- has now been observed in a wide spectrum of hematologic disorders. However, most cases had either preleukemia (39%) or leukemia (46%). When detected during preleukemia, the 5q- usually appeared alone (74%), while during overt leukemia it regularly was accompanied by other abnormalities (88%).
Humic-like substances of bacterial origin. II. Fractionation of the bacterial humic-like substances by gel filtration on sephadex gels. (1977)

Humic-like substances obtained from cells of Pseudomonas acidovorans were separated on Sephadex G-25 into two groups of substances of different molecular weight. The substances of the molecular weight greater than 5000 were successively separated on Sephadex gels G-50, G-75, G-100. Five fractions of different molecular weight were obtained, the percentage of which varied depending on the media used and time of incubation of the bacteria. Most (38%--46%) of the compounds contained in the bacterial humic acids were of approximate molecular weight of 40 000--50 000. The distribution of the fractions in the bacterial "humic-acids" was compared with those of the humic acid made by Fluka A. G. The synthetic humic acid contained most (approximately 40%) of the compounds of approximate molecular weight of 8000--10 000. In the bacterial and synthetic material the content of the compounds with the molecular weight above 100 000 was very similar (8%--12%).
A polarization-independent distributed Bragg reflector based on phase-shifted grating structures (1996)

A polarization-independent narrow-band Bragg reflector based on a novel phase-shifted grating structure is proposed and analyzed. Operation and design principles for the proposed grating structure as an polarization-independent optical filter are described. Robustness of the polarization-independent filter against modal birefringence and polarization effects in grating couplings and modal losses are examined and verified. Tunability of the polarization-independent filter is also studied and demonstrated.
Anti-Human Immunodeficiency Virus Hematopoietic Progenitor Cell-Delivered Ribozyme in a Phase I Study: Myeloid and Lymphoid Reconstitution in Human Immunodeficiency Virus Type-1–Infected Patients (2004)

A phase I gene transfer clinical study was undertaken to examine the ability to introduce a potential anti-human immunodeficiency virus (HIV) gene therapeutic into hematopoietic progenitor cells (HPC), thereby contributing to multilineage engraftment. The potential therapeutic effect of genetically modifying HPC with protective genes in HIV-infected adults depends in part on the presence of adult thymic activity and myeloid capacity in the setting of HIV replication. Herein we report the presence and expression of a retroviral vector encoding an anti-HIV-1 ribozyme in mature hematopoietic cells of different lineages, and de novo T-lymphocyte development ensuing from genetically engineered CD34(+) HPC. Sustained output of vector-containing mature myeloid and T-lymphoid cells was detected even in patients with multidrug-resistant infection. In addition, the study showed that the degree of persistence of gene-containing cells was dependent on transduced HPC dose. These novel findings support the concept of gene therapy as a modality to effect immune reconstitution with cells engineered to inhibit HIV replication and this report represents the first demonstration of long-term maintenance of a potential therapeutic transgene in HIV disease.
The inhibitory potential of Fc receptor homolog 4 on memory B cells (2003)

Fc receptor homolog 4 (FcRH4) is a B cell-specific member of the recently identified family of FcRHs whose intracellular domain contains three potential immunoreceptor tyrosine-based inhibitory motifs (ITIMs). The signaling potential of this receptor, shown here to be preferentially expressed by memory B cells, was compared with the inhibitory receptor FcgammaRIIb in B cells expressing either WT FcgammaRIIb or chimeric proteins in which the intracellular domain of FcRH4 was fused to the transmembrane and extracellular domains of FcgammaRIIb. Coligation of the FcgammaRIIb/FcRH4 chimeric protein with the B cell receptor (BCR) led to tyrosine phosphorylation of the two membrane-distal tyrosines and profound inhibition of BCR-mediated calcium mobilization, whole cell tyrosine phosphorylation, and mitogen-activated protein (MAP)-kinase activation. Mutational analysis of the FcRH4 cytoplasmic region indicated that the two membrane-distal ITIMs are essential for this inhibitory potential. Phosphopeptides corresponding to these ITIMs could bind the Src homology 2 (SH2) domain-containing tyrosine phosphatases SHP-1 and SHP-2, which associated with the WT FcRH4 and with mutants having inhibitory capability. These findings indicate the potential for FcRH4 to abort B cell receptor signaling by recruiting SHP-1 and SHP-2 to its two membrane distal ITIMs.
Fluorine in Organic Chemistry (2004)

General discussion of organic fluorine chemistry Preparation of highly fluorinated compounds Partial or selective fluorination The influence of fluorine of fluorocarbon groups on some reaction centres Nucleophilic displacement of halogen from fluorocarbon systems Elimination reactions Polyfluoroalkanes, polyfluoroalkenes, and derivatives Functional compounds containing oxygen, sulphur, or nitrogen and their derivatives Polyfluoroaromatic compounds Organometallic reagents References Index
Molecular and Functional Characterization of a Family of Rat Brain T-type Calcium Channels (2001)

Voltage-gated calcium channels represent a heterogenous family of calcium-selective channels that can be distinguished by their molecular, electrophysiological, and pharmacological characteristics. We report here the molecular cloning and functional expression of three members of the low voltage-activated calcium channel family from rat brain (alpha(1G), alpha(1H), and alpha(1I)). Northern blot and reverse transcriptase-polymerase chain reaction analyses show alpha(1G), alpha(1H), and alpha(1I) to be expressed throughout the newborn and juvenile rat brain. In contrast, while alpha(1G) and alpha(1H) mRNA are expressed in all regions in adult rat brain, alpha(1I) mRNA expression is restricted to the striatum. Expression of alpha(1G), alpha(1H), and alpha(1I) subunits in HEK293 cells resulted in calcium currents with typical T-type channel characteristics: low voltage activation, negative steady-state inactivation, strongly voltage-dependent activation and inactivation, and slow deactivation. In addition, the direct electrophysiological comparison of alpha(1G), alpha(1H), and alpha(1I) under identical recording conditions also identified unique characteristics including activation and inactivation kinetics and permeability to divalent cations. Simulation of alpha(1G), alpha(1H), and alpha(1I) T-type channels in a thalamic neuron model cell produced unique firing patterns (burst versus tonic) typical of different brain nuclei and suggests that the three channel types make distinct contributions to neuronal physiology.
Vitreous: an inhibitor of retinal extract-induced neovascularization. (1983)

One of the major problems in assessing neovascularization in mammalian experimental animal models is the immunologic response of the host to stimuli from nonautologous species. Hence, crude bovine vitreous and retinal extracts may produce a complex immune reaction when tested in the rabbit. To circumvent this problem, the chicken chorioallantoic membrane (CAM) assay is most appropriate. In this study the CAM assay for angiogenesis has been modified to study antiangiogenic substances. The modified assay is described in detail and used to demonstrate for the first time the inhibition by adult bovine vitreous of neovascularization induced by extracts of adult bovine retina. In addition to vitreous, three common glycosaminoglycans (keratan sulfate, chondroitin sulfate C, and hyaluronic acid) were assayed for antiangiogenic activity. The results indicate that vitreous inhibition of retinal extract-induced neovascularization is dose dependent, while the sulfated glycosaminoglycans tested had no antiangiogenic activity. A commercial preparation of bovine vitreous hyaluronic acid exhibited a slight, but not statistically significant, inhibitory activity. When vitreous extracts were digested with hyaluronidase, no loss of antiangiogenic activity occurred. These results suggest that the inhibitor of angiogenesis from adult vitreous is probably not a common glycosaminoglycan. The results are consistent with the hypothesis that antiangiogenic substance(s) in vitreous and angiogenic components from retina may act as natural antagonists in controlling the process of retinal neovascularization.
Acellular Pertussis Vaccine Booster Combined With Diphtheria and Tetanus Toxoids for Adolescents (2006)

In adolescents, the studied Tdap was safe and immunogenic and induced pertussis antibodies that were higher than those associated with efficacy in infants.
Comparison between p-nitrophenyl glucuronide and phenolphthalein glucuronide as substrates in the assay of beta-glucuronidase. (1967)

The p -nitrophenyl glucuronide method for the determination of β-glucuronidase activity is compared with the phenolphthalein glucuronide method in a variety of diseases. It is shown that linear correlation exists between the two methods. The presence of isoenzymes, which would hydrolyze the substrates at different rates, is therefore excluded. The reaction conditions for the phenolphthalein glucuronide method are investigated and improved upon. Normal values for both methods in milliunits per milliliter are presented. The advantages of the p-nitrophenyl glucuronide method are indicated.
The isomorphous structures of prethrombin2, hirugen–, and PPACK–thrombin: Changes accompanying activation and exosite binding to thrombin (1994)

The X-ray crystal structure of prethrombin2 (pre2), the immediate inactive precursor of alpha-thrombin, has been determined at 2.0 A resolution complexed with hirugen. The structure has been refined to a final R-value of 0.169 using 14,211 observed reflections in the resolution range 8.0-2.0 A. A total of 202 water molecules have also been located in the structure. Comparison with the hirugen-thrombin complex showed that, apart from the flexible beginning and terminal regions of the molecule, there are 4 polypeptide segments in pre2 differing in conformation from the active enzyme (Pro 186-Asp 194, Gly 216-Gly 223, Gly 142-Pro 152, and the Arg 15-Ile 16 cleavage region). The formation of the Ile 16-Asp 194 ion pair and the specificity pocket are characteristic of serine protease activation with the conformation of the catalytic triad being conserved. With the determination of isomorphous structures of hirugen-thrombin and D-Phe-Pro-Arg chloromethyl ketone (PPACK)-thrombin, the changes that occur in the active site that affect the kinetics of chromogenic substrate hydrolysis on binding to the fibrinogen recognition exosite have been determined. The backbone of the Ala 190-Gly 197 segment in the active site has an average RMS difference of 0.55 A between the 2 structures (about 3.7 sigma compared to the bulk structure). This segment has 2 type II beta-bends, the first bend showing the largest shift due to hirugen binding. Another important feature was the 2 different conformations of the side chain of Glu 192. The side chain extends to solvent in hirugen-thrombin, which is compatible with the binding of substrates having an acidic residue in the P3 position (protein-C, thrombin platelet receptor). In PPACK-thrombin, the side chain of Asp 189 and the segment Arg 221A-Gly 223 move to provide space for the inhibitor, whereas in hirugen-thrombin, the Ala 190-Gly 197 movement expands the active site region. Although 8 water molecules are expelled from the active site with PPACK binding, the inhibitor complex is resolvated with 5 other water molecules.
Impaired nuclear factor erythroid 2-related factor 2 expression increases apoptosis of airway epithelial cells in patients with chronic obstructive pulmonary disease due to cigarette smoking (2016)

Nrf2 expression was lower in COPD patients than in control subjects. Nrf2 might have a protective role against apoptosis caused by CSE-induced oxidative stress. These results suggest an involvement of Nrf2 in COPD and administration of antioxidants to patients with COPD might be a basic therapeutic option.
A rare case of giant dermoid cyst with ipsilateral paratubal cystadenoma during pregnancy (2017)

Dermoid cysts are considered the most common ovarian cysts in adolescents and pregnant women. In rare cases, they can attain a huge size. Paratubal cysts are also common in adolescents. They are usually simple cysts present in the broad ligament. In this case, we report a giant dermoid cyst with ipsilateral paratubal serous cystadenoma discovered during pregnancy of a 20-year-old primigravida. Both cysts were managed conservatively, and then removed successfully at the time of cesarean section by cystectomy.
Efficient memory simulation in SimICS (2002)

We describe novel techniques used for efficient simulation of memory in SimICS; an instruction level simulator developed at SICS. The design has focused on efficiently supporting the simulation of multiprocessors, analyzing complex memory hierarchies and running large binaries with a mixture of system level and user level code. A software caching mechanism (the Simulator Translation Cache, STC) improves the performance of interpreted memory operations by reducing the number of calls to complex memory simulation code. Major data structures are allocated lazily to reduce the size of the simulator process. A well defined internal interface to generic memory simulation simplifies user extensions. Leveraging on a flexible interpreter based on threaded code allows runtime selection of statistics gathering, memory profiling, and cache simulation with low overhead. The result is a memory simulation scheme that supports a range of features for use in computer architecture research, program profiling, and debugging.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibition of Angiogenic Properties of Brain Endothelial Cells by Platelet-Derived Sphingosine-1-Phosphate (2005)

The platelet-derived lysophospholipid sphingosine-1-phosphate (S1P) is present in blood plasma and is one of the most potent growth factors displaying proangiogenic activity towards endothelial cells (EC) derived from various tissues. The paracrine regulation of brain angiogenesis by platelet-derived growth factors is, however, poorly understood. In the present study, we assessed the role of S1P on brain EC migration and tubulogenesis, using rat brain-derived (RBE4) EC as an in vitro model. We show that S1P inhibits brain EC migration and tubulogenesis, while it displays proangiogenic activity towards noncerebral EC. Overexpression of the S1P receptor S1P-1 in RBE4 cells potentiated all of the S1P-mediated events. We also show that the lack of expression of MT1-MMP, a membrane-bound matrix metalloproteinase that is thought to cooperate with S1P in tubulogenic processes, may explain the antiangiogenic activity of S1P on brain vasculature. Altogether our results support the hypothesis of a tissue-specific, antiangiogenic role of S1P in the brain, which may help to stabilize the cerebral vasculature and thus have crucial impact on the setting and regulation of normal brain vascularization.
Acidic Mammalian Chitinase Is Not a Critical Target for Allergic Airway Disease (2011)

The expression of acidic mammalian chitinase (AMCase) is associated with Th2-driven respiratory disorders. To investigate the potentially pathological role of AMCase in allergic airway disease (AAD), we sensitized and challenged mice with ovalbumin or a combination of house dust mite (HDM) plus cockroach allergen. These mice were treated or not treated with small molecule inhibitors of AMCase, which significantly reduced allergen-induced chitinolytic activity in the airways, but exerted no apparent effect on pulmonary inflammation per se. Transgenic and AMCase-deficient mice were also submitted to protocols of allergen sensitization and challenge, yet we found little or no difference in the pattern of AAD between mutant mice and wild-type (WT) control mice. In a separate model, where mice were challenged only with intratracheal instillations of HDM without adjuvant, total bronchoalveolar lavage (BAL) cellularity, inflammatory infiltrates in lung tissues, and lung mechanics remained comparable between AMCase-deficient mice and WT control mice. However BAL neutrophil and lymphocyte counts were significantly increased in AMCase-deficient mice, whereas concentrations in BAL of IL-13 were significantly decreased compared with WT control mice. These results indicate that, although exposure to allergen stimulates the expression of AMCase and increased chitinolytic activity in murine airways, the overexpression or inhibition of AMCase exerts only a subtle impact on AAD. Conversely, the increased numbers of neutrophils and lymphocytes in BAL and the decreased concentrations of IL-13 in AMCase-deficient mice challenged intratracheally with HDM indicate that AMCase contributes to the Th1/Th2 balance in the lungs. This finding may be of particular relevance to patients with asthma and increased airway neutrophilia.