gebhart/patrepeval huggingface dataset:
Dietary mannan-oligosaccharides and their effect on chicken caecal microflora in relation to Salmonella Enteritidis colonization (2002)

This study first investigates the effects of mash diet, or mash supplemented with either 2.5% mannose-oligosaccharide (MOS) or palm kernel meal (PKM), on the microflora of the hen caecal contents. Second, it investigates the effect of caecal contents of hens (HCC) fed mash or mash supplemented with MOS or PKM on the major microflora groups of chicks, and their inhibitory effect on Salmonella enterica serovar Enteritidis (PT4) colonization. Finally, this study investigates the effect over time of diets supplemented with MOS or PKM on S. Enteritidis colonization and the microflora of chicks. In hens, supplemented diets increased Bifidobacterium spp., while decreasing members of Enterobacteriaceae and Enterococcus spp., compared with the mash diet. Chicks dosed with the HCC showed, on average, increased numbers of anaerobes, while the numbers of aerobes decreased including coliforms and S. Enteritidis compared with controls without HCC. In chicks fed the MOS-supplemented or PKM-supplemented diets, S. Enteritidis colonization decreased over time, compared with mash alone. Four-week-old PKM birds showed an increase in Bifidobacterium spp. and Lactobacillus spp., with a decrease in S. Enteritidis compared with week 2. Generally, the HCC and diets supplemented with MOS or PKM affected the birds intestinal microflora by increasing the Bifidobacterium spp. and Lactobacillus spp., while decreasing the Enterobacteriaceae groups. They also reduced susceptibility in young chickens to colonization by S. Enteritidis.
45nm CMOS 8&amp;#x03A9; Class-D audio driver with 79% efficiency and 100dB SNR (2010)

A direct battery connect (2.35 V to 5.5 V) 100 dB SNR Class-D audio driver in 45 nm CMOS is presented. At 3.5 V supply, 525 mW is delivered into an 8 Ω load with 79% efficiency.
Electron microscope studies on polyethylene and polypropylene (1962)

Abstract Replication techniques for electron microscopy have been used to relate the microstructural characteristics and physical properties of polyethylene and polypropylene. This study included polymer particles and molded pads. The low penetrating power and damage from heating prevents the direct examination of polymer particles in the microscope. Replication, however, has given details of the surface structure of these particles. The spherulitie structure of these polymers in molded form has been determined by replicating etched surfaces. Marked differences in the spherulitic structure of polyethylene and polypropylene have been observed The effect of molecular weight on spherulitic structure of both polymers has also been established.
Structures of the Ribosome in Intermediate States of Ratcheting (2009)

Protein biosynthesis on the ribosome requires repeated cycles of ratcheting, which couples rotation of the two ribosomal subunits with respect to each other, and swiveling of the head domain of the small subunit. However, the molecular basis for how the two ribosomal subunits rearrange contacts with each other during ratcheting while remaining stably associated is not known. Here, we describe x-ray crystal structures of the intact Escherichia coli ribosome, either in the apo-form (3.5 angstrom resolution) or with one (4.0 angstrom resolution) or two (4.0 angstrom resolution) anticodon stem-loop tRNA mimics bound, that reveal intermediate states of intersubunit rotation. In the structures, the interface between the small and large ribosomal subunits rearranges in discrete steps along the ratcheting pathway. Positioning of the head domain of the small subunit is controlled by interactions with the large subunit and with the tRNA bound in the peptidyl-tRNA site. The intermediates observed here provide insight into how tRNAs move into the hybrid state of binding that precedes the final steps of mRNA and tRNA translocation.
Characterization of the enterocyte-like brush border cytoskeleton of the C2BBe clones of the human intestinal cell line, Caco-2 (1992)

The brush border (BB) of the enterocyte is a well-studied example of the actin-based cytoskeleton. We describe here a cell culture model that expresses a faithful representation of the in vivo structure. Two clones (C2BBe 1 and 2) isolated from the cell line Caco-2 (derived from a human colonic adenocarcinoma) formed a polarized monolayer with an apical BB morphologically comparable to that of the human colon. BBs could be isolated by standard methods and contained the microvillar proteins villin, fimbrin, sucrase-isomaltase and BB myosin I, and the terminal web proteins fodrin and myosin II. The immunolocalization of these proteins in confluent, filter-grown monolayers was determined by laser scanning confocal microscopy; patterns of distribution comparable to those in human enterocytes were observed. Sedimentation analysis of cell homogenates derived from C2BBe cells and human colonic epithelial cells demonstrated similar patterns of fractionation of BB proteins; the physical association of those proteins, as determined by extraction from the BB, was also comparable between the two cell types. Like enterocytes of the human intestine, C2BBe cells expressed multiple myosin I immunogens reactive with a head domain-specific monoclonal antibody raised against avian BB myosin I, one of which co-migrated with the approximately 110 kilodalton (kDa) heavy chain of human BB myosin I. In addition, the C2BBe cells express a pair of higher molecular mass immunogens (130 and 140 kDa). These myosin I immunogens all exhibit ATP-dependent association with the C2BBe cytoskeleton. Although the higher molecular mass immunogens were detected in several other human intestinal lines examined, including the parent Caco-2 line, none of these other lines expressed detectable levels of the 110 kDa immunogen, which is presumed to be the heavy chain of human BB myosin I.
Formation of Extracellular Sphingolipids by Microorganisms (1962)

Tetraacetylphytosphingosine (TAPS) formation by the F-60-10 mating type strain of the yeast Hansenula ciferrii, previously observed on agar plates, has been shown to take place in submerged cultures. The optimal conditions for TAPS formation, and the correlation of TAPS production and sugar utilization under aerobic conditions, were studied in 10-liter fermentors. For each gram of glucose consumed, 5 mg of TAPS were formed; for each gram of yeast solids produced, 15 mg of TAPS were synthesized. A 750-liter pilot-plant run yielded 175 g of crude TAPS, which were obtained by hexane extraction of centrifuged yeast cells.
Identification of Catabolite Repression as a Physiological Regulator of Biofilm Formation by<i>Bacillus subtilis</i>by Use of DNA Microarrays (2003)

Biofilms are structured communities of cells that are encased in a self-produced polymeric matrix and are adherent to a surface. Many biofilms have a significant impact in medical and industrial settings. The model gram-positive bacterium Bacillus subtilis has recently been shown to form biofilms. To gain insight into the genes involved in biofilm formation by this bacterium, we used DNA microarrays representing >99% of the annotated B. subtilis open reading frames to follow the temporal changes in gene expression that occurred as cells transitioned from a planktonic to a biofilm state. We identified 519 genes that were differentially expressed at one or more time points as cells transitioned to a biofilm. Approximately 6% of the genes of B. subtilis were differentially expressed at a time when 98% of the cells in the population were in a biofilm. These genes were involved in motility, phage-related functions, and metabolism. By comparing the genes differentially expressed during biofilm formation with those identified in other genomewide transcriptional-profiling studies, we were able to identify several transcription factors whose activities appeared to be altered during the transition from a planktonic state to a biofilm. Two of these transcription factors were Spo0A and sigma-H, which had previously been shown to affect biofilm formation by B. subtilis. A third signal that appeared to be affecting gene expression during biofilm formation was glucose depletion. Through quantitative biofilm assays and confocal scanning laser microscopy, we observed that glucose inhibited biofilm formation through the catabolite control protein CcpA.
MEMS Gyroscope with Less than 1-deg/h Bias Instability Variation in Temperature Range from —40 °C to 125 °C (2017)

We developed a gyroscope with less than 1-deg/h bias instability variation in a temperature range from -40 °C to 125 °C while performing around 4-deg/h bias instability. This stability was achieved by using the stable frequency separation between the drive and sense modes of a Coriolis vibratory gyroscope. To achieve this stability, the mechanical part was designed with a one-sided open frame to mitigate the variation of resonant frequencies caused by thermal stress. At the circuit level, we implemented a self-clocking architecture with a bandpass Σ - Δ analog-to-digital converter to maintain low quantization noise level over the operational temperature range. The fabricated gyroscope demonstrated a 2-Hz variation of frequency separation for an operational frequency of 18.5 kHz in the operational temperature range. At a system level, a bias instability variation of 0.9 deg/h in the temperature range while performing bias instability less than 4.21 deg/h was demonstrated. This low-noise variation is potentially beneficial for applications requiring a Kalman filter, such as GPS-denied navigation systems, that demands a precise and predetermined noise property.
A 3-level re-encryption model to ensure data protection in cloud computing environments (2014)

Ensuring about the security and privacy of stored data in cloud servers is one of the most challenging issues that decrease the rate of reliability in cloud computing environments. Applying cryptography algorithms is the most common solution to enhance the reliability of cloud servers and to protect resources from possible attacks and un-predictable events. However, the security of this type of protection is affected when some users are revoked by data owner from accessing to data. Hence, an efficient and reliable re-encryption model based on multi-level cryptography has been introduced in this paper to prevent un-authorized accesses from revoked users to cloud-based resources. The main aim of the proposed model is to classify data to several levels for managing the process of re-encryption more efficient and reliable. Therefore, 3 levels of security have been defined to carry out this classification according to the security characteristics of stored data: Time-Based Level, High Risk Level, and Custom Level. The presented model has been evaluated according to three parameters: performance, security, and scalability. The evaluation process was done by establishing a simulated environment to investigate functionality of re-encryption procedure in each level of security. Functionality and security analysis of this model shows that, the reliability and efficiency of data protection process in cloud computing environments is improved considerably by using 3-level re-encryption model.
On Service Resilience in Cloud-Native 5G Mobile Systems (2016)

To cope with the tremendous growth in mobile data traffic on one hand, and the modest average revenue per user on the other hand, mobile operators have been exploring network virtualization and cloud computing technologies to build cost-efficient and elastic mobile networks and to have them offered as a cloud service. In such cloud-based mobile networks, ensuring service resilience is an important challenge to tackle. Indeed, high availability and service reliability are important requirements of carrier grade, but not necessarily intrinsic features of cloud computing. Building a system that requires the five nines reliability on a platform that may not always grant it is, therefore, a hurdle. Effectively, in carrier cloud, service resilience can be heavily impacted by a failure of any network function (NF) running on a virtual machine (VM). In this paper, we introduce a framework, along with efficient and proactive restoration mechanisms, to ensure service resilience in carrier cloud. As restoration of a NF failure impacts a potential number of users, adequate network overload control mechanisms are also proposed. A mathematical model is developed to evaluate the performance of the proposed mechanisms. The obtained results are encouraging and demonstrate that the proposed mechanisms efficiently achieve their design goals.
Molecular cloning, cDNA sequencing, and chemical synthesis of cecropin B from Hyalophora cecropia. (1985)

Two cDNA clones containing coding information for cecropin B from the Cecropia moth (Hyalophora cecropia) were identified by means of a synthetic probe. Sequencing of the two inserts showed that cecropin B is processed from a 62-amino acid residue precursor molecule including a 26-residue leader peptide and a COOH-terminal glycine residue. The latter presumably donates the nitrogen of the amide group present on the COOH-terminal leucine residue of the mature cecropin B. The sequence deduced for the mature cecropin B differed in the COOH-terminal region from the tentative structure previously determined by carboxypeptidase digestion. To settle the discrepancy, cecropin B was synthesized according to the cDNA sequence with an amidated COOH-terminal leucine. Natural and synthetic cecropin B were found to be indistinguishable with respect to electrophoretic mobility and antibacterial activity against seven different bacteria. The COOH-terminal tetrapeptides were isolated from both natural and synthetic cecropin B and found to be indistinguishable. The correct sequence for cecropin B is (formula; see text).
Measurement of electric field by interferometric spectral trace observation (2005)

We present a new methodology that obtains, in an analytical way, the complex electric field of ultrashort pulses. This methodology is based only on Fourier analysis of the frequency components of spectrally resolved interferometric collinear autocorrelations. We present an experimental demonstration of this technique and the results are compared with the conventional second-harmonic generation frequency-resolved optical gating technique.
Implementation of an active optical range sensor using laser slit for in-door intelligent mobile robot (2002)

The sensor with real-time environment recognition ability is one of the key technologies for autonomous robots. The authors have designed and implemented a small size optical range sensor for their experimental mobile robot. The sensor consists of a laser slit generator, a CCD image sensor and a processing unit. Using this sensor, the real-time obstacle avoiding function is realized and added to the autonomous navigation aspect of the robot.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The use of polylactic acid matrix and periosteal grafts for the reconstruction of rabbit knee articular defects (1991)

In order to find a material that would improve cartilage repair, we investigated the use of porous polylactic acid matrix (PLA) with and without periosteal grafts in large articular defects in the medial femoral condyles of 18 New Zealand white rabbit knees. The right knee defect was filled with PLA, the left defect was filled with PLA and a periosteal graft. All animals were killed at 12 weeks. PLA allowed for the de novo growth of neocartilage at the articular surface in all specimens and appeared to serve as a scaffolding for cell migration and matrix formation. Histologically, small amounts of PLA remained under the neocartilage with the majority being replaced by bone. PLA was a suitable carrier for periosteal grafts with a high graft survival rate (89%) and proliferation of a neocartilage which was thicker and more closely resembled articular cartilage than PLA alone knees. Biochemically, there was more type II collagen in the grafted knees (83%) than in the PLA alone knees (65%). Biomechanical tests of the neocartilage included equilibrium displacement, aggregate modulus, and apparent permeability. These tests were not statistically different between PLA alone and grafted knees. Comparison to normal cartilage indicated that the neocartilage was less stiff but had similar permeability. A consistent repair of the articular defects was achieved with and without periosteal grafts resulting in a tissue that closely resembled hyaline articular cartilage.
NMR Structural Studies of Interactions of a Small, Nonpeptidyl Tpo Mimic with the Thrombopoietin Receptor Extracellular Juxtamembrane and Transmembrane Domains (2007)

Thrombopoietin (Tpo) is a glycoprotein growth factor that supports hematopoietic stem cell survival and expansion and is the principal regulator of megakaryocyte growth and differentiation. Several small, nonpeptidyl molecules have been identified as selective human Tpo receptor (hTpoR) agonists. To understand how the small molecule Tpo mimic SB394725 interacts and activates hTpoR, we performed receptor domain swap and mutagenesis studies. The results suggest that SB394725 interacts specifically with the extracellular juxtamembrane region (JMR) and the transmembrane (TM) domain of hTpoR. Solution and solid-state NMR structural studies using a peptide containing the JMR-TM sequences showed that this region of hTpoR, unexpectedly, consists of two alpha-helices separated by a few nonhelical residues. SB394725 interacts specifically with His-499 in the TM domain and a few distinct residues in the JMR-TM region and affects several specific C-terminal TM domain residues. The unique structural information provided by these studies both sheds light on the distinctive mechanism of action of SB394725 and provides valuable insight into the mechanism of ligand-induced cytokine receptor activation.
Dysregulated Hepatic Methionine Metabolism Drives Homocysteine Elevation in Diet-Induced Nonalcoholic Fatty Liver Disease (2015)

Methionine metabolism plays a central role in methylation reactions, production of glutathione and methylarginines, and modulating homocysteine levels. The mechanisms by which these are affected in NAFLD are not fully understood. The aim is to perform a metabolomic, molecular and epigenetic analyses of hepatic methionine metabolism in diet-induced NAFLD. Female 129S1/SvlmJ;C57Bl/6J mice were fed a chow (n = 6) or high-fat high-cholesterol (HFHC) diet (n = 8) for 52 weeks. Metabolomic study, enzymatic expression and DNA methylation analyses were performed. HFHC diet led to weight gain, marked steatosis and extensive fibrosis. In the methionine cycle, hepatic methionine was depleted (30%, p< 0.01) while s-adenosylmethionine (SAM)/methionine ratio (p< 0.05), s-adenosylhomocysteine (SAH) (35%, p< 0.01) and homocysteine (25%, p< 0.01) were increased significantly. SAH hydrolase protein levels decreased significantly (p <0.01). Serine, a substrate for both homocysteine remethylation and transsulfuration, was depleted (45%, p< 0.01). In the transsulfuration pathway, cystathionine and cysteine trended upward while glutathione decreased significantly (p< 0.05). In the transmethylation pathway, levels of glycine N-methyltransferase (GNMT), the most abundant methyltransferase in the liver, decreased. The phosphatidylcholine (PC)/ phosphatidylethanolamine (PE) ratio increased significantly (p< 0.01), indicative of increased phosphatidylethanolamine methyltransferase (PEMT) activity. The protein levels of protein arginine methytransferase 1 (PRMT1) increased significantly, but its products, monomethylarginine (MMA) and asymmetric dimethylarginine (ADMA), decreased significantly. Circulating ADMA increased and approached significance (p< 0.06). Protein expression of methionine adenosyltransferase 1A, cystathionine β-synthase, γ-glutamylcysteine synthetase, betaine-homocysteine methyltransferase, and methionine synthase remained unchanged. Although gene expression of the DNA methyltransferase Dnmt3a decreased, the global DNA methylation was unaltered. Among individual genes, only HMG-CoA reductase (Hmgcr) was hypermethylated, and no methylation changes were observed in fatty acid synthase (Fasn), nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (Nfκb1), c-Jun, B-cell lymphoma 2 (Bcl-2) and Caspase 3. NAFLD was associated with hepatic methionine deficiency and homocysteine elevation, resulting mainly from impaired homocysteine remethylation, and aberrancy in methyltransferase reactions. Despite increased PRMT1 expression, hepatic ADMA was depleted while circulating ADMA was increased, suggesting increased export to circulation.
Secretory Granule Content Proteins and the Luminal Domains of Granule Membrane Proteins Aggregate in Vitro at Mildly Acidic pH (1996)

A major unresolved issue in the field of secretory granule biogenesis is the extent to which the aggregation of granule content proteins is responsible for the sorting of regulated from constitutively secreted proteins. The aggregation process is postulated to take place in the trans-Golgi network and immature secretory granules as the proteins encounter mildly acidic pH and high calcium concentrations. We have developed in vitro assays that reconstitute the precipitation out of solution of secretory granule content proteins of anterior pituitary gland and adrenal medulla. In the assays, all of the major granule content polypeptides form a precipitate as the pH is titrated below 6.5, and this precipitate can be recovered in the pellet fraction after centrifugation. Addition of calcium is required for the aggregation of chromaffin granule content. In contrast to the proteins secreted by the regulated pathway, the constitutively secreted proteins IgG, albumin, and angiotensinogen, when added to the assays, remain predominantly in the supernatant. Among the individual proteins tested, prolactin is found to aggregate homophilically under these conditions and can drive the co-aggregation of other proteins, such as the chromogranins. Soluble forms of granule membrane proteins, including dopamine beta-hydroxylase and peptidyl glycine alpha-amidating enzyme also co-aggregated with granule content proteins. The results are consistent with the idea that spontaneous aggregation of proteins occurring under ionic conditions similar to those at the sites of granule formation is a property restricted to those proteins packaged in secretory granules. In addition, the association of luminal domains of membrane proteins with content proteins in vitro raises the possibility that analogous interactions between membrane-bound and content proteins also occur during granule formation in intact cells.
Palladium-Catalyzed Negishi Cross-Coupling Reactions of Unactivated Alkyl Iodides, Bromides, Chlorides, and Tosylates (2003)

A single method (2% Pd(2)(dba)(3)/8% PCyp(3)/NMI in THF/NMP at 80 degrees C; Cyp = cyclopentyl) achieves the cross-coupling of a range of beta-hydrogen-containing primary alkyl iodides, bromides, chlorides, and tosylates with an array of alkyl-, alkenyl-, and arylzinc halides. The process is compatible with a variety of functional groups, including esters, amides, imides, nitriles, and heterocycles.