gebhart/patrepeval huggingface dataset:
CRISPR-mediated gene silencing reveals involvement of the archaeal S-layer in cell division and virus infection (2019)

The S-layer is a proteinaceous surface lattice found in the cell envelope of bacteria and archaea. In most archaea, a glycosylated S-layer constitutes the sole cell wall and there is evidence that it contributes to cell shape maintenance and stress resilience. Here we use a gene-knockdown technology based on an endogenous CRISPR type III complex to gradually silence slaB, which encodes the S-layer membrane anchor in the hyperthermophilic archaeon Sulfolobus solfataricus. Silenced cells exhibit a reduced or peeled-off S-layer lattice, cell shape alterations and decreased surface glycosylation. These cells barely propagate but increase in diameter and DNA content, indicating impaired cell division; their phenotypes can be rescued through genetic complementation. Furthermore, S-layer depleted cells are less susceptible to infection with the virus SSV1. Our study highlights the usefulness of the CRISPR type III system for gene silencing in archaea, and supports that an intact S-layer is important for cell division and virus susceptibility.
In vivo assessment of the significance of phosphorylation of the Arabidopsis chloroplast protein import receptor, atToc33 (2005)

atToc33 is a transit peptide receptor of the chloroplast outer envelope membrane, and possesses GTPase activity. In vitro, its transit peptide- and GTP-binding properties are abrogated by its phosphorylation at serine 181, which was proposed to represent an important regulatory mechanism. We mutated S181 to alanine (to prevent phosphorylation), and to aspartate and glutamate (to mimic the effects of phosphoserine), and expressed all three proteins in ppi1 (atToc33 knockout) plants using the native promoter. The mutants complemented ppi1 with equal efficiency in respect of all criteria tested, including protein import efficiency and light stress tolerance. The data suggest that atToc33 phosphorylation may not play an important role in vivo.
A Quick Guide to Software Licensing for the Scientist-Programmer (2012)

Computing is ubiquitous in every domain of scientific research. Software is the means by which scientists harness the power of computers, and much scientific computing relies on software conceived and developed by other practicing researchers. The task of creating scientific software, however, does not end with the publication of computed results. Making the developed software available for inspection and use by other scientists is essential to reproducibility, peer-review, and the ability to build upon others’ work. In fulfilling expectations to distribute and disseminate their software, scientist-programmers are required to be not only proficient scientists and coders, but also knowledgeable in legal strategies for licensing their software. Navigating the often complex legal landscape of software licensing can be overwhelming, even for sophisticated programmers. Institutional technology transfer offices (TTOs) exist to help address this need, but due to mismatches in expectations or specific domain knowledge, interactions between scientists and TTO staff can result in suboptimal outcomes. As practitioners in the scientific computing and technology law fields, we have witnessed firsthand the confusion and difficulties associated with licensing scientifically generated software. Together, we offer a primer on software licensing with a focus on the particular needs of the scientist-software developer in choosing a software license and engaging with TTOs.
Optimal Backup Policies for a Database System with Incremental Backup (2002)

Abstract When the data of a database are frequently updated, the operation of incremental or cumulative backup is usually adopted so as to make the backup copies efficiently. Such backups are suitably executed between the operations of complete backup for most mass database systems. This paper considers three backup policies for two schemes of export backup in a database system: The reliability measures of these policies are derived, using the theory of cumulative processes. Comparisons between two schemes of export backup are made. Specifically, an optimal backup scheme and an optimal time of a full backup are discussed. © 2001 Scripta Technica, Electron Comm Jpn Pt 3, 85(4): 1–9, 2002
Glow discharge amorphous silicon tin alloys (1984)

We present basic density of states, photoresponse, and transport measurements made on low bandgap a-SiSn:H alloys produced by RF glow discharge deposition of SiH/sub 4/, H/sub 2/ and Sn(CH/sub 3/)/sub 4/. Although we demonstrate major changes in the local bonding structure and the density of states, the normalized photoresponse still remains poor. We provide evidence that two types of defect levels are produced with Sn alloying, and that the resultant density of states increase explains not only the n- to p-type conductivity transition reported earlier, but also the photoresponse behavior. We also report that a-SiSn:H can be doped with P. From our device analysis we suggest that in order to improve the alloy performance significantly, the density of states should be decreased to levels comparable to or lower than those presently obtained in a-Si:H.
Super-Resolution Imaging Spectroscopy (1994)

Among the remaining challenges facing chemical analysis is the capability of extending to micro-scale samples the spectacular detection limits that have been achieved for a variety of spectroscopic methods. In such samples, a vanishingly small quantity of target analyte material, relative to background, presents a serious obstacle to achieving the rate of detection improvement that the scientific community has come to expect over the past two decades. However, a variety of problems from cell biology, electronics technology, and materials science continue to require what is best described as micro-trace composition determination. In addition, the efforts to determine the properties of single discrete entities (cells, for example) have attracted substantial interest, with much remaining room for improvement. The direction for research seeking to make this improvement is suggested from the lessons derived from successful single-atom and single-molecule detection. These milestones of spectroscopy have been achieved almost entirely by using readily available detection technology while minimizing background levels. The lesson from the progress in both fields is the axiom Anything can be detected if the background is low enough.
Optical control of neuronal growth (2004)

Understanding and controlling neuronal growth are basic objectives in neuroscience, biology, biophysics, and biomedicine, and are vital for the formation of neural circuits in vitro, as well as for nerve regeneration in vivo. All molecular stimuli for neuronal growth eventually address the polymeric cytoskeleton, which advances a neurite's leading edge also known as the growth cone. We have shown that optical forces of a highly focused infrared laser beam influence the motility of a growth cone by biasing the polymerization-driven intracellular machinery. In actively extending growth cones, a laser spot placed at specific areas of the neurite's leading edge affects the growth speed, the direction taken by a growth cone, and the splitting of a growth cone. This novel optical tool manipulates a natural biological process, the cytoskeleton driven morphological changes in growth cones, with potential applications in the formation of neuronal networks and in understanding growth cone motility. The current apparatus combines optical tweezers, phase contrast and fluorescence imaging, and real-time shape detection. Automated and dynamically readjusted irradiation of the growth cone is used to examine and to influence structural and morphological changes of neuronal growth.
Transverse modes in large-mode-area fibers (2010)

Thesis (Ph. D.)--University of Rochester. Dept. of Physics and Astronomy, 2010.
RF-Link for Cortical Neuroprosthesis (2005)

This paper describes an RF-link system suitable for intracortical neuroprosthesis. The wireless coupling minimizes the risk of infection and improves the patient health level. Data and power are transmitted by means of an RF low-coupling transformer. Binary FSK modulation is used in the forward link (from outside to implanted prosthesis) and BPSK is used in the backward link (implanted prosthesis to outside). Experimental results are presented, and important concerns regarding the magnetic coupling are addressed.
Hypermethylated SFRP2 gene in fecal DNA is a high potential biomarker for colorectal cancer noninvasive screening (2008)

Hypermethylation of SFRP2 gene in fecal DNA is a novel molecular biomarker of CRC and carries a high potential for the remote detection of CRC and premalignant lesions as noninvasive screening method.
Dynamic tire friction models for vehicle traction control (2003)

We derive a dynamic friction force model for road/tire interaction for ground vehicles. The model is based on a similar dynamic friction model for contact developed previously for contact-point friction problems, called the LuGre model. We show that the dynamic LuGre friction model is able to accurately capture velocity and road/surface dependence of the tire friction force.
The Brain of the Planarian as the Ancestor of the Human Brain (1985)

The planarian is the simplest living animal having a body plan of bilateral symmetry and cephalization. The brain of these free-living flatworms is a bilobed structure with a cortex of nerve cells and a core of nerve fibres including some that decussate to form commissures. Special sensory input from chemoreceptors, photoreceptor cells of primitive eyes, and tactile receptors are integrated to provide motor responses of the entire body, and local reflexes. Many morphological, electrophysiological, and pharmacological features of planarian neurons, as well as synaptic organization, are reminiscent of the vertebrate brain. Multipolar neurons and dendritic spines are rare in higher invertebrates, but are found in the planarian. Several neurotransmitter substances identified in the human brain also occur in the planarian nervous system. The planarian evolved before the divergence of the phylogenetic line leading to vertebrates. This simple worm therefore is suggested as a living example of the early evolution of the vertebrate brain. An extraordinary plasticity and regenerative capacity, and sensitivity to neurotoxins, provide unique opportunities for studying the reorganization of the nervous system after injury. Study of this simple organism may also contribute to a better understanding of the evolution of the human nervous system.
Antenna Live: FlyBot (2013)

How do you make a robot that can fly itself? Are there benefits to allowing semi-autonomous robots in our skies? Who will be at the controls of these craft? &lt;br/&gt;&lt;br/&gt;The HALO Unmanned Aerial System was the top scorer at the DARPA UAVForge Challenge in 2012. Meet the team from the University of Southampton who built HALO from scratch&lt;br/&gt;&lt;br/&gt;
A State of the Art Review on Emotional Speech Databases (2003)

Thirty-two emotional speech databases are reviewed. Each database consists of a corpus of human speech pronounced under different emotional conditions. A basic description of each database and its applications is provided. The conclusion of this study is that automated emotion recognition on these databases cannot achieve a correct classification that exceeds 50 % for the four basic emotions, i.e., twice as much as random selection. Second, natural emotions cannot be easily classified as simulated ones (i.e., acting) can be. Third, the most common emotions searched for in decreasing frequency of appearance are anger, sadness, happiness, fear, disgust, joy, surprise, and boredom.
Kinetic modeling as a tool to understand the influence of cell culture process parameters on the glycation of monoclonal antibody biotherapeutics (2019)

Glycation, the nonenzymatic reaction between the reducing sugar glucose and the primary amine residues on amino acid side chains, commonly occurs in the cell culture supernatant during production of therapeutic monoclonal antibodies (mAbs). While glycation has the potential to impact efficacy and pharmacokinetic properties for mAbs, the most common undesirable impact of glycation is on the distribution of charged species, often a release specification for commercial processes. Existing empirical approaches are usually insufficient to rationalize the effects of cell line and process changes on glycation. To address this gap, we developed a kinetic model for estimating mAb glycation levels during the cell culture process. The rate constant for glycation, including temperature and pH dependence, was estimated by fitting the kinetic model to time-course glycation data from bioreactors operated at different process settings that yielded a wide range of glycation values. The parameter values were further validated by independently estimating glycation rate constants using cell-free incubation studies at various temperatures. The model was applied to another mAb, by re-estimating the activation energy to account for effect of a glycation "hotspot". The model was further utilized to study the role of temperature shift as an approach to reduce glycation levels in the manufacturing process for mAb2. While a downshift in temperature resulted in lowering of glycation levels for mAb2, the model helped elucidate that this effect was caused due to contribution from changes in glucose consumption, mAb secretion and temperature, instead of a direct impact of temperature alone on the kinetic rate of glycation.
The antidiabetic gutsy role of metformin uncovered? (2013)

International audience
Cryoheater as a means of cryosurgery control (2003)

A new concept for cryosurgery control is presented in this paper, a concept which has the potential to dramatically change the outcome of cryosurgery. Unlike other cryosurgery control techniques, which are based on controlling the thermal performance of the cryoprobe, this new concept is based on heating the treated tissue as a means of shaping the frozen region. The new controlling heater is termed a 'cryoheater'. The cryoheater is a complementary device to the cryoprobe and can work with any cryosurgery cooling technique. In the current pilot study, the new cryoheater is demonstrated in a gelatin solution and, using heat transfer simulations, it is studied in simulated cases of prostate cryosurgery. It is suggested that cryosurgery planning tools and optimization techniques must be developed before the concept of the cryoheater can be applied in its full capacity.
Investigations on the Nature of the Auxin-Wave in the Cambial Region of Pine Stems (1987)

The major auxin of Scots pine (Pinus silvestris L.) which is transported basipetally into agar strips from the cambial region of the stem was quantified by the Went Avena coleoptile curvature assay before and after reversed phase C(18) high performance liquid chromatography (HPLC), and then identified by full spectrum gas chromatography-mass spectrometry (GC-MS) as indole-3-acetic acid (IAA). The IAA was subsequently quantified by GC-MS-selected ion monitoring (SIM) using an internal standard of [(13)C]-(C(6))-IAA. The amount of IAA collected into 22-millimeter long agar strips during 10 minutes of contact with the stem cambial region was estimated by GC-MS-SIM and the Went bioassay to be 2.3 and 2.1 nanograms per strip, respectively. The GC-MS technique thus confirmed the results obtained by the Went curvature assay. The Avena curvature assay revealed the presence of at least one other, more polar (based on HPLC retention time) auxin that diffused into the agar strips with the IAA. Its bioactivity was only 5% of the IAA fraction. Its HPLC retention time was earlier than IAA-glucoside, IAA-aspartate, or IAA-glycine, but the same as IAA-inositol. No significant amounts of inhibitors or synergists of IAA activity on the Avena assay were found in extracts corresponding to one or five strips of agar. Thus, the direct bioassay of the agar strips immediately after their removal from the cambial region of P. silvestris stem sections reflects the concentration of the native IAA. For both P. silvestris and lodgepole pine (Pinus contorta) a wavelike pattern of auxin stimulation of Avena curvature was found in agar strips exposed for only 10 minutes to the basal ends of an axial series of 6-millimeter long sections from the cambial region of the stem. This wavelike pattern was subsequently confirmed for P. contorta both by Avena curvature assay and by GC-MS-SIM of HPLC fractions at the retention time of [(3)H]IAA. The wavelike pattern of auxin diffusing from the cambial region of Pinus has thus been determined to consist primarily of IAA and this pattern has now been quantitated using both the Went Avena curvature assay and GC-MS-SIM with [(13)C]-C(6)-IAA as an internal standard.
Upper-Limb Evolution and Development: Skeletons in the Closet (2009)

1Robert A. Chase Hand and Upper Limb Center, Department of Orthopaedic Surgery, Stanford University, 770 Welch Road, Suite 400, Palo Alto, CA 94304. E-mail address: [email protected]
Late chronic catechin antioxidant treatment is deleterious to the endothelial function in aging mice with established atherosclerosis (2010)

Various antioxidants, including polyphenols, prevent the development of atherosclerosis in animal models, contrasting with the failure of antioxidants to provide benefits in patients with established atherosclerosis. We therefore tested in a mouse model the hypothesis that although catechin is atheroprotective in prevention, catechin brings no global vascular protection when initiated after established atherosclerosis, because aging associated with dyslipidemia has induced irreversible dysfunctions. To this end, LDLr(-/-); hApoB(+/+) atherosclerotic (ATX, 9 mo old) and pre-ATX (3 mo old) male mice were treated with catechin (30 mg x kg(-1) x day(-1)) up to 12 mo of age. Vascular function and endothelium/leukocyte interactions were studied at 12 mo old. The renal artery endothelium-dependent dilations were impaired with age whereas adhesion of leukocytes onto the native aortic endothelium was increased (P < 0.05). Aortic oxidative stress [reactive oxygen species (ROS)] increased (P < 0.05) at 3 mo in ATX and at 12 mo in wild-type mice. Aorta mRNA expression of NADPH oxidase increased, whereas that of manganese superoxide dismutase decreased in 12-mo-old ATX mice only. In mice with established ATX, catechin (from 9 to 12 mo) reduced (P < 0.05) by approximately 60% ROS without affecting plaque burden. Notably, catechin worsened endothelial dysfunction and further increased leukocyte adhesion (P < 0.05) in ATX mice. In contrast, the same catechin treatment reversed all age-related dysfunctions in wild-type mice. On the other hand, in pre-ATX mice treated for 9 mo with catechin, plaque burden was reduced by 64% (P < 0.05) and all vascular markers were normalized to the 3-mo-old values. These results demonstrate that an antioxidant treatment is deleterious in mice with established atherosclerosis.
Isolation and characterization of antineoplastic alkaloids from <i>Catharanthus roseus</i> l. Don. cultivated in Egypt (2010)

Vinblastine and vincristine (the antileukemic agents) were isolated, in a pure form, from Catharanthus roseus L. Don., cultivated in Egypt, by several chromatographic techniques. Five modified methods for the preparation of total alkaloids were carried out. All the isolated mixtures were evaluated by HPLC and HPTLC analyses. The antineoplastic alkaloids; vinblastine and vincristine, were isolated by the use of vacuum liquid chromatographic column on silica gel : aluminium oxide (1:1) mixed bed vacuum liquid chromatography (VLC), Charcoal column, and finally purified by centrifugally accelerated radial chromatography (Chromatotrone).
2P2-B14 Gait Identification using Video Sequential Images for Person Following : Identification based on back view of walking (2008)

There is gait identification as the personal authentication technology. Gait identification to find an outsider and to recognize a suspicious figure has ever proposed. On the other hand, in order for the mobile robot to extend the place of activity, technology for person following is useful. So, in this paper, gait identification for person following is proposed.
A Flow Cytometry-Based Assay for Quantifying Non-Plaque Forming Strains of Yellow Fever Virus (2012)

Primary clinical isolates of yellow fever virus can be difficult to quantitate by standard in vitro methods because they may not form discernable plaques or induce a measurable cytopathic effect (CPE) on cell monolayers. In our hands, the Dakar strain of yellow fever virus (YFV-Dakar) could not be measured by plaque assay (PA), focus-forming assay (FFA), or by measurement of CPE. For these reasons, we developed a YFV-specific monoclonal antibody (3A8.B6) and used it to optimize a highly sensitive flow cytometry-based tissue culture limiting dilution assay (TC-LDA) to measure levels of infectious virus. The TC-LDA was performed by incubating serial dilutions of virus in replicate wells of C6/36 cells and stained intracellularly for virus with MAb 3A8.B6. Using this approach, we could reproducibly quantitate YFV-Dakar in tissue culture supernatants as well as from the serum of viremic rhesus macaques experimentally infected with YFV-Dakar. Moreover, the TC-LDA approach was >10-fold more sensitive than standard plaque assay for quantitating typical plaque-forming strains of YFV including YFV-17D and YFV-FNV (French neurotropic vaccine). Together, these results indicate that the TC-LDA technique is effective for quantitating both plaque-forming and non-plaque-forming strains of yellow fever virus, and this methodology may be readily adapted for the study and quantitation of other non-plaque-forming viruses.
Caveolin‐1 deficiency decreases atherosclerosis by hampering leukocyte influx into the arterial wall and generating a regulatory T‐cell response (2011)

Caveolin-1 plays a crucial role in atherosclerosis, which is mainly attributed to its effects on low-density-lipoprotein (LDL) transcytosis. However, caveolin-1 has also been implicated in the regulation of inflammation. We investigated the effects of caveolin-1 deficiency in atherosclerosis with its accompanying changes in plaque- and lymphoid-related immunology and inflammation. Cav1(-/-)Apoe(-/-) mice exhibited a 15-fold reduction in plaque size with plaques containing fewer macrophages, T cells, and neutrophils. Intravital microscopy revealed 83% less leukocyte adhesion to the vessel wall in Cav1(-/-)Apoe(-/-) mice, which could be attributed to reduced endothelial chemokine ligand-2 (CCL-2/MCP-1) and vascular cell adhesion molecule-1 (VCAM-1) expression. Caveolin-1 deficiency resulted in a 57% increase in regulatory T cells and a 4% decrease in CD4(+) effector T cells in lymphoid organs. Bone marrow transplantations revealed that Cav1(-/-)Apoe(-/-) mice receiving Cav1(+/+)Apoe(-/-) or Cav1(-/-)Apoe(-/-) bone marrow presented 4- to 4.5-fold smaller plaques with no additional phenotypic changes. In contrast, atherosclerosis was not affected in Cav1(+/+) Apoe(-/-) recipients receiving Cav1(-/-)Apoe(-/-) or Cav1(+/+) Apoe(-/-) bone marrow. However, the presence of Cav1(-/-) Apoe(-/-) bone marrow was associated with an anti-inflammatory T-cell profile. Our study reveals that nonhematopoietic caveolin-1 determines plaque size, whereas hematopoietic caveolin-1 regulates lymphoid immune-modulation. However, both are required for phenotypic modulation of plaques.