gebhart/patrepeval huggingface dataset:
Genetically edited pigs lacking CD163 show no resistance following infection with the African swine fever virus isolate, Georgia 2007/1 (2016)

African swine fever is a highly contagious, often fatal disease of swine for which there is no vaccine or other curative treatment. The macrophage marker, CD163, is a putative receptor for African swine fever virus (ASFV). Pigs possessing a complete knockout of CD163 on macrophages were inoculated with Georgia 2007/1, a genotype 2 isolate. Knockout and wild type pen mates became infected and showed no differences in clinical signs, mortality, pathology or viremia. There was also no difference following in vitro infection of macrophages. The results do not rule out the possibility that other ASFV strains utilize CD163, but demonstrate that CD163 is not necessary for infection with the Georgia 2007/1 isolate. This work rules out a significant role for CD163 in ASFV infection and creates opportunities to focus on alternative receptors and entry mechanisms.
Cloning and Expression of the Growth Hormone-Dependent Insulin-Like Growth Factor-Binding Protein (1988)

N-terminal as well as internal amino acid sequence data were obtained from the GH dependent, insulin-like growth factor (IGF) binding protein, BP-53, purified from human plasma. Based on these sequence data, full-length cDNA clones of BP-53 have been isolated, and the complete deduced sequence of BP-53 determined. This sequence contains a 27 amino acid putative signal sequence followed by a mature protein of 264 amino acids containing 18 cysteine residues clustered near the N- and C-terminus. The deduced protein sequence of BP-53 has 33% amino acid identity including conservation of all 18 cysteine residues with the recently cloned BP-28, a smaller human IGF-binding protein identified in amniotic fluid and also secreted by the cell line HEP G2. Expression of the cloned BP-53 cDNA in mammalian tissue culture cells results in secretion of the protein into the culture medium. This expressed protein is identical to plasma-derived BP-53 in its immunoreactivity, high affinity binding of IGF-I and IGF-II, and mobility on sodium dodecyl sulfate gel electrophoresis.
CEACAM1, a Cell-Cell Adhesion Molecule, Directly Associates with Annexin II in a Three-dimensional Model of Mammary Morphogenesis (2003)

The epithelial cell adhesion molecule CEACAM1 (carcinoembryonic antigen cell adhesion molecule-1) is down-regulated in colon, prostate, breast, and liver cancer. Here we show that CEACAM1-4S, a splice form with four Ig-like ectodomains and a short cytoplasmic domain (14 amino acids), directly associates with annexin II, a lipid raft-associated molecule, which is also down-regulated in many cancers. Annexin II was identified using a glutathione S-transferase pull-down assay in which the cytoplasmic domain of CEACAM-4S was fused to glutathione S-transferase, the fusion protein was incubated with cell lysates, and isolated proteins were sequenced by mass spectrometry. The interaction was confirmed first by reciprocal immunoprecipitations using anti-CEACAM1 and anti-annexin II antibodies and second by confocal laser microscopy showing co-localization of CEACAM1 with annexin II in mammary epithelial cells grown in Matrigel. In addition, CEACAM1 co-localized with p11, a component of the tetrameric AIIt complex at the plasma membrane, and with annexin II in secretory vesicles. Immobilized, oriented peptides from the cytoplasmic domain of CEACAM1-4S were shown to directly associate with bovine AIIt, which is 98% homologous to human AIIt, with average KD values of about 30 nM using surface plasmon resonance, demonstrating direct binding of functionally relevant AIIt to the cytoplasmic domain of CEACAM1-4S.
An anti-Hick's effect in monkey and human saccade reaction times (2008)

In order to execute movements to targets in the environment, we must first select a target in which to move, generally from an array of alternatives. Hick's Law states that reaction time (RT) increases as the number of response alternatives increases. Violations of this law, however, generally in the form of the absence of a relationship between response alternatives and RT have been reported in the literature. K. Kveraga, L. Boucher, and H. C. Hughes (2002), for example, found that saccades to visual targets violate Hick's Law. To examine this violation further, we measured saccade RTs in monkeys and humans and found that saccade RTs actually decreased as the number of potential target locations increased. We hypothesize that this arises because subjects must actively inhibit premature saccades, and that the required inhibition increases as the certainty of a movement to a particular location increases. With increased inhibition, saccade onset is delayed, resulting in an anti-Hick's effect.
Sampling from a moving window over streaming data (2002)

We introduce the problem of sampling from a moving window of recent items from a data stream and develop two algorithms for this problem. The first algorithm, chain-sample, extends reservoir sampling to deal with the expiration of data elements from the sample. The expected memory usage of our algorithm is O(k) when maintaining a sample of size k over a window of the n most recent elements from the data stream, and with high probability the algorithm requires no more than O(k log n) memory.When the number of elements in the window is variable, as is the case when the size of the window is defined as a time duration rather than as a fixed number of data elements, the sampling problem becomes harder. Our second algorithm, priority-sample, works even when the number of elements in the window can vary dynamically over time. With high probability, the priority-sample algorithm uses no more than O(k log n) memory.
Analysis of the requirements for parathyroid hormone action in renal membranes with the use of inhibiting analogues. (1975)

&lt;p&gt;For the exhibition &lt;em&gt;A History of Irritated Material&lt;/em&gt;, Raven Row commissioned the translation into English of part of Suely Rolnik’s compendious research project &lt;em&gt;Lygia Clark, from Object to Event&lt;/em&gt;, an archive of video interviews on Lygia Clark, focusing on her late project &lt;em&gt;Structuring the Self&lt;/em&gt; (1977–87), the culmination of Clark’s life-art. Raven Row hosted a discussion between Guy Brett, close friend of Lygia Clark and one of the key interpreters of her work, and Lars Bang Larsen, curator of the exhibition, who has written extensively about Rolnik’s project. The discussion considered Lygia Clark’s radical proposals involving the body in its sensory and sensual capacities, and Suely Rolnik’s attempt to reactivate Clark’s ideas via a ‘living archive.’&lt;/p&gt;\n
Polymers as Dewetting Agents (1998)

We study the stability of a film of poly(dimethylsiloxane) with an oligomer as the solvent. On a silanated Si−wafer, the solvent wets, but the polymer does not. We find that at all polymer volume fraction φ, films below a critical thickness ec(φ) are unstable. We observe two regimes of dewetting vs φ: (i) classical "dry" dewetting for φ > φL, where the film ruptures in a multitude of droplets on a dry solid; (ii) unusual "wet" dewetting for φ < φL, where the final droplets coexist with a film of pure solvent. In this new regime, ec(φ) is found to scale like φ0.80±0.01. We interpret these results via an equilibrium between droplets of solution and a solid covered by a film of pure solvent. This equilibrium occurs if φ < φL, the critical concentration. At φ = φL we have a "leak out" transition of the solvent. All these results can be extended to other complex systems, where wetting processes and phase separation are coupled.
Microsporidian mitosomes retain elements of the general mitochondrial targeting system (2006)

Microsporidia are intracellular parasites that infect a variety of animals, including humans. As highly specialized parasites, they are characterized by a number of unusual adaptations, many of which are manifested as extreme reduction at the molecular, biochemical, and cellular levels. One interesting aspect of reduction is the mitochondrion. Microsporidia were long considered to be amitochondriate, but recently a tiny mitochondrion-derived organelle called the mitosome was detected. The molecular function of this organelle remains poorly understood. The mitosome has no genome, so it must import all its proteins from the cytosol. In other fungi, the mitochondrial protein import machinery consists of a network series of heterooligomeric translocases and peptidases, but in microsporidia, only a few subunits of some of these complexes have been identified to date. Here, we look at targeting sequences of the microsporidian mitosomal import system and show that mitosomes do in some cases still use N-terminal and internal targeting sequences that are recognizable by import systems of mitochondria in yeast. Furthermore, we have examined the function of the inner membrane peptidase processing enzyme and demonstrate that mitosomal substrates of this enzyme are processed to mature proteins in one species with a simplified processing complex, Antonospora locustae. However, in Encephalitozoon cuniculi, the processing complex is lost altogether, and the preprotein substrate functions with the targeting leader still attached. This report provides direct evidence for presequencing processing in mitosomes and also shows how a complex molecular system has continued to degenerate throughout the evolution of microsporidia.
What is a Plant Cell? Continued. (1991)

What is a Plant Cell? ContinuedAre animal and plant cells so different that there should be different definitions for the limits of their cells?A "no" answer is certainly reasonable, but Andrew Staehelin (What is a Plant Cell?A Response, 1991, Plant Cell 3, 553) should have acknowledged that many prominent plant biologists have answered "yes."What an animal biologist or a microbiologist refers to as a "cell," the unit bounded by the plasma membrane, a traditional plant biologist would cal1 the "protoplast."Many plant biologists reserve the term "cell" for the protoplast and the cell wall.No less authorities on plant cells than Katherine Esau and Ray Evert explicitly define the term this way (K.
A Single-Chain Fv Diabody against Human Leukocyte Antigen-A Molecules Specifically Induces Myeloma Cell Death in the Bone Marrow Environment (2007)

Cross-linked human leukocyte antigen (HLA) class I molecules have been shown to mediate cell death in neoplastic lymphoid cells. However, clinical application of an anti-HLA class I antibody is limited by possible side effects due to widespread expression of HLA class I molecules in normal tissues. To reduce the unwanted Fc-mediated functions of the therapeutic antibody, we have developed a recombinant single-chain Fv diabody (2D7-DB) specific to the alpha2 domain of HLA-A. Here, we show that 2D7-DB specifically induces multiple myeloma cell death in the bone marrow environment. Both multiple myeloma cell lines and primary multiple myeloma cells expressed HLA-A at higher levels than normal myeloid cells, lymphocytes, or hematopoietic stem cells. 2D7-DB rapidly induced Rho activation and robust actin aggregation that led to caspase-independent death in multiple myeloma cells. This cell death was completely blocked by Rho GTPase inhibitors, suggesting that Rho-induced actin aggregation is crucial for mediating multiple myeloma cell death. Conversely, 2D7-DB neither triggered Rho-mediated actin aggregation nor induced cell death in normal bone marrow cells despite the expression of HLA-A. Treatment with IFNs, melphalan, or bortezomib enhanced multiple myeloma cell death induced by 2D7-DB. Furthermore, administration of 2D7-DB resulted in significant tumor regression in a xenograft model of human multiple myeloma. These results indicate that 2D7-DB acts on multiple myeloma cells differently from other bone marrow cells and thus provide the basis for a novel HLA class I-targeting therapy against multiple myeloma.
Design and Synthesis of Pyrrolidine-5,5-trans-lactams (5-Oxohexahydropyrrolo[3,2-b]pyrroles) as Novel Mechanism-Based Inhibitors of Human Cytomegalovirus Protease. 2. Potency and Chirality (2001)

The stereospecific synthesis of a series of alpha-methylpyrrolidine-5,5-trans-lactam inhibitors of human cytomegalovirus (HCMV) protease is described. Examination of the SAR in this series has defined the size and chirality of the alpha-substituent, optimized the acyl substituent on the lactam nitrogen, and defined the steric constraint of this functionality. The SAR of the functionality on the pyrrolidine nitrogen of the trans-lactam has been investigated, and this has led to the discovery of potent serine protease inhibitors that are highly selective for the viral enzyme over the mammalian enzymes elastase, thrombin, and acetylcholine esterase. The mechanism of action of our lead compounds has been established by mass spectrometry, and enzymatic degradation of HCMV deltaAla protease acylated with these inhibitors showed that Ser 132 is the active site nucleophile. The crystal structure of HCMV protease was obtained and used to model the conformationally restricted, chiral (S)-proline-alpha-methyl-5,5-trans-lactams into the active site groove of the enzyme, enabling us to direct and rationalize the SAR in this series. The activity against HCMV deltaAla protease is the greatest with inhibitors based on the dansyl-(S)-proline alpha-methyl-5,5-trans-lactam template, which have low nanomolar activity against the viral enzyme.
Pain relief using continuous bupivacaine infusion in the paravertebral space after loin incision. (2004)

Paravertebral blockade using bupivacaine is an effective and safe method for pain relief following renal surgery through loin incision.
A spontaneous murine melanoma lung metastasis comprised of host x tumor hybrids. (2000)

Cells from a lung metastasis, arising from Cloudman S91 melanoma cells implanted s.c. in the tail of a BALB/c nu/nu mouse, were comprised chiefly of host x tumor hybrids. These lung metastasis cells showed: (a) 30-40% increased DNA content; (b) resistance to 10(-4) M hypoxanthine, 4 x 10(-7) M aminopterin, and 1.6 x 10(-5) M thymidine (HAT) + G418; and (c) the presence in genomic DNA of genes for both wt and albino tyrosinase, reflecting the DBA/2J (Cloudman S91) and BALB/c mouse genotypes, respectively. Individual clones of lung metastasis cells expressed enhanced pigmentation, motility, and responsiveness to MSH/IBMX, a behavior similar to that recently reported for artificially generated melanoma x macrophage fusion hybrids. These similarities suggested that the host fusion partner generating the lung metastasis hybrids might have been a macrophage, although formal proof for this was not possible. The results provide the first direct evidence that host x tumor hybridization could serve as an initiating mechanism for melanoma metastasis.
Nitro: a capacity-optimized SSD cache for primary storage (2014)

For many primary storage customers, storage must bal-ance the requirements for large capacity, high perfor-mance, and low cost. A well studied technique is to place a solid state drive (SSD) cache in front of hard disk drive (HDD) storage, which can achieve much of the perfor-mance benefit of SSDs and the cost per gigabyte effi-ciency of HDDs. To further lower the cost of SSD caches and increase effective capacity, we propose the addition of data reduction techniques. Our cache architecture, called Nitro, has three main contributions: (1) an SSD cache design with adjustable deduplication, compression, and large replacement units, (2) an evaluation of the trade-offs between data re-duction, RAM requirements, SSD writes (reduced up to 53%, which improves lifespan), and storage perfor-mance, and (3) acceleration of two prototype storage sys-tems with an increase in IOPS (up to 120%) and reduc-tion of read response time (up to 55%) compared to an SSD cache without Nitro. Additional benefits of Nitro include improved random read performance, faster snap-shot restore, and reduced writes to SSDs. 1
Behavior, body composition, and vascular phenotype of homocystinuric mice on methionine‐restricted diet or enzyme replacement therapy (2019)

Classic homocystinuria (HCU) is an inherited disorder characterized by elevated homocysteine (Hcy) in plasma and tissues resulting from cystathionine β-synthase (CBS) deficiency. There is no cure, and patients are predominantly managed by methionine-restricted diet (MRD) to limit the production of Hcy. In this study, we used the I278T mouse model of HCU to evaluate the long-term impact of a novel enzyme replacement therapy [truncated human CBS C15S mutant modified with linear 20-kDa <i>N</i>-hydroxysuccinimide ester polyethylene glycol (OT-58)] on clinical end points relevant to human patients with HCU. In addition, we compared its efficacy on a background of either MRD or normal methionine intake [regular diet (REG)] to that of MRD alone. We found that, compared with untreated I278T mice, OT-58 treatment of I278T mice fed with the REG diet resulted in a 90% decrease in plasma Hcy concentrations and correction of learning/cognition, endothelial dysfunction, hemostasis, bone mineralization, and body composition. On background of the MRD, OT-58 performed equally well with plasma Hcy entirely normalized. The MRD alone decreased plasma Hcy by 67% and corrected the HCU phenotype in I278T mice. However, the MRD increased anxiety and reduced bone mineral content in both I278T mice and wild-type controls. This study shows that OT-58 is a highly efficacious novel treatment for HCU on the background of either normal or restricted methionine intake.-Majtan, T., Park, I., Cox, A., Branchford, B. R., di Paola, J., Bublil, E. M., Kraus, J. P. Behavior, body composition, and vascular phenotype of homocystinuric mice on methionine-restricted diet or enzyme replacement therapy.
Analysis of the receptor-ligand interactions in the natural killer–mediated lysis of freshly isolated myeloid or lymphoblastic leukemias: evidence for the involvement of the Poliovirus receptor (CD155) and Nectin-2 (CD112) (2004)

On the basis of recent clinical and experimental data, natural killer (NK) cells appear to play a crucial role in eradication of acute myeloid leukemias. In the present study, by exploiting our current knowledge on NK receptors and their ligands on target cells, we investigated the interactions between NK and leukemic cells. We show that the size of the NK cell subset expressing the killer immunoglobulin-like receptor (KIR) not engaged by the HLA-class I alleles of the patient parallels the degree of NK cytotoxicity against leukemic cells. A sharp down-regulation of HLA-class I molecules has been detected in various leukemias and it was more frequent in myeloid than in lymphoblastic leukemias. Analysis of the ligands for triggering NK receptors revealed the consistent expression of Poliovirus receptor (PVR) and Nectin-2 in myeloid leukemias. In contrast, major histocompatibility complex class I-related chain molecules A/B (MICA/B) and UL1b-binding protein (ULBPs) were either absent or weakly expressed. Accordingly, NK-mediated lysis of these leukemias was dependent on DNAM-1 but not NKG2D. The major role of NKp46 and NKp30 was also confirmed. The expression of PVR and/or Nectin-2 was less frequent in lymphoblastic leukemias. In most leukemias, both CD48 and NTBA were down-regulated. The correlation found between marker expression and susceptibility to lysis may reveal useful information for NK-based immunotherapy.
T-cell receptor gamma delta and gamma transgenic mice suggest a role of a gamma gene silencer in the generation of alpha beta T cells. (1990)

A T lymphocyte expresses on its surface one of two types of antigen receptor, T-cell receptor alpha beta or T-cell receptor gamma delta, encoded by a pair of somatically rearranged alpha and beta or gamma and delta genes. It has been suggested that alpha beta T cells are generated only from precursor T cells that failed to rearrange gamma and delta genes in a functional form. However, we found that transgenic mice constructed with functionally rearranged gamma and delta genes produce a normal number of alpha beta T cells. The transgene gamma present in these alpha beta T cells is repressed apparently through an associated cis DNA element (silencer). We propose that some T-cell precursors are committed to generate alpha beta T cells independent of the rearrangement status of their gamma gene and that this commitment involves activation of a factor(s) that interacts with the gamma gene-associated silencer.
Differential phase contrast in optical coherence tomography (1999)

We report on a modification of optical coherence tomography (OCT) that allows one to measure small phase differences between beams traversing adjacent areas of a specimen. The sample beam of a polarization-sensitive low-coherence interferometer is split by a Wollaston prism into two components that traverse the object along closely spaced paths. After reflection at the various sample surfaces, the beams are recombined at the Wollaston prism. Any phase difference encountered between the two beams is converted into a change of polarization state of the recombined beam. This change is measured, and the resulting signals are converted to differential phase-contrast OCT images. The first images obtained from simple test objects allowed us to determine path-difference gradients with a resolution of the order of 5×10-5.
Potential Sexual Transmission of Zika Virus (2015)

In December 2013, during a Zika virus (ZIKV) outbreak in French Polynesia, a patient in Tahiti sought treatment for hematospermia, and ZIKV was isolated from his semen. ZIKV transmission by sexual intercourse has been previously suspected. This observation supports the possibility that ZIKV could be transmitted sexually.
MMAS-1, the Branch Point Between cis- and trans-Cyclopropane-containing Oxygenated Mycolates in Mycobacterium tuberculosis (1997)

The proportion of mycolic acid containing trans-substituents at the proximal position of the meromycolate chain is an important determinant of fluidity of the mycobacterial cell wall and is directly related to the sensitivity of mycobacterial species to hydrophobic antibiotics. MMAS-1, an enzyme encoded in the gene cluster responsible for the biosynthesis of methoxymycolates, was overexpressed in Mycobacterium tuberculosis and shown to result in the overproduction of trans-cyclopropane and trans-olefin-containing oxygenated mycolic acids. MMAS-1 converted a cis-olefin into a trans-olefin with concomitant introduction of an allylic methyl branch in a precursor to both the methoxy and ketone-containing mycolic acids. In addition to an increase in the amount of trans-mycolate, MMAS-1 expression resulted in a substantial increase in the amount of ketomycolate produced relative to methoxymycolate. Thus MMAS-1 may act at a complex branch point where expression of this enzyme directly affects the cis- to trans-ratio and indirectly affects the keto to methoxy ratio. Overexpression of MMAS-1 resulted in a substantially slower growth rate at moderately elevated temperature, decreased thermal stability of the cell wall as measured by differential scanning calorimetry, and an increased permeability to chenodeoxycholate. These results provide experimental evidence for the intermediacy of trans-olefinic mycolate precursors in trans-cyclopropane formation and suggest that increasing the proportion of the polar ketomycolate subclass may exert a significant fluidizing effect on the cell wall.