gebhart/patrepeval huggingface dataset:
Virulence of the Emerging Pathogen, Burkholderia Pseudomallei , Depends Upon the O -linked Oligosaccharyltransferase, PglL (2020)

<b>Aim:</b> We sought to characterize the contribution of the <i>O</i>-OTase, PglL, to virulence in two <i>Burkholderia</i> spp. by comparing isogenic mutants in <i>Burkholderia pseudomallei</i> with the related species, <i>Burkholderia thailandensis</i>. <b>Materials & methods:</b> We utilized an array of <i>in vitro</i> assays in addition to <i>Galleria mellonella</i> and murine <i>in vivo</i> models to assess virulence of the mutant and wild-type strains in each <i>Burkholderia</i> species. <b>Results:</b> We found that <i>pglL</i> contributes to biofilm and twitching motility in both species. <i>PglL</i> uniquely affected morphology; cell invasion; intracellular motility; plaque formation and intergenus competition in <i>B. pseudomallei</i>. This mutant was attenuated in the murine model, and extended survival in a vaccine-challenge experiment. <b>Conclusion:</b> Our data support a broad role for <i>pglL</i> in bacterial fitness and virulence, particularly in <i>B. pseudomallei</i>.
Combination of two anti‐CD5 monoclonal antibodies synergistically induces complement‐dependent cytotoxicity of chronic lymphocytic leukaemia cells (2013)

The treatment of chronic lymphocytic leukaemia (CLL) has been improved by introduction of monoclonal antibodies (mAbs) that exert their effect through secondary effector mechanisms. CLL cells are characterized by expression of CD5 and CD23 along with CD19 and CD20, hence anti-CD5 Abs that engage secondary effector functions represent an attractive opportunity for CLL treatment. Here, a repertoire of mAbs against human CD5 was generated and tested for ability to induce complement-dependent cytotoxicity (CDC) and antibody-dependent cell-mediated cytotoxicity (ADCC) both as single mAbs and combinations of two mAbs against non-overlapping epitopes on human CD5. The results demonstrated that combinations of two mAbs significantly increased the level of CDC compared to the single mAbs, while no enhancement of ADCC was seen with anti-CD5 mAb combinations. High levels of CDC and ADCC correlated with low levels of Ab-induced CD5 internalization and degradation. Importantly, an anti-CD5 mAb combination enhanced CDC of CLL cells when combined with the anti-CD20 mAbs rituximab and ofatumumab as well as with the anti-CD52 mAb alemtuzumab. These results suggest that an anti-CD5 mAb combination inducing CDC and ADCC may be effective alone, in combination with mAbs against other targets or combined with chemotherapy for CLL and other CD5-expressing haematological or lymphoid malignancies.
Interaction of viruses with annexins: a potential therapeutic target? (2000)

This review elaborates on the known interactions of annexins with some viral pathogens of man. The best documented interactions are those between human cytomegalovirus and annexin II, and hepatitis B virus and annexin V. The review starts with a description of some structural considerations and potential functions of these annexins before going into a more detailed analysis of the viral interactions themselves. Finally, some questions relating to the suitability of these interactions as a drug target are touched upon.
Enhancement of plasmid-mediated gene therapy for muscular dystrophy by directed plasmid integration (2005)

Plasmid-mediated gene therapy can restore dystrophin expression in skeletal muscle in the mdx mouse, a model of Duchenne muscular dystrophy. However, sufficient long-term expression and distribution of dystrophin remain a hurdle for translating this technology into a viable treatment for Duchenne muscular dystrophy. To improve plasmid-mediated gene therapy for muscle diseases, we studied the effects of targeted plasmid integration using a phage integrase (phiC31) that can mediate the integration of suitably modified plasmids into the mammalian genome. Using a luciferase expression plasmid, we monitored plasmid gene expression noninvasively in living mice by bioluminescence imaging. Coinjection of an integrase plasmid resulted in 5- to 10-fold higher levels of sustained luciferase expression. Likewise, plasmid-mediated dystrophin expression in mdx muscle was enhanced by integration. Using a combination of dystrophin and luciferase plasmids, we analyzed the functional benefit of dystrophin expression in the dystrophic muscle. The expression of dystrophin slowed the loss of luciferase expression associated with muscle degeneration, and that protection was enhanced by targeted integration of the dystrophin plasmid. In the presence of integrase, dystrophin expression was distributed along a much greater length of individual fibers, and this was associated with increased protection against degenerative changes. These data demonstrate the importance of both the level and distribution of dystrophin expression to achieve therapeutic efficacy, and that the efficacy can be enhanced by targeted plasmid integration.
Cache-Aided Communications in MISO Networks with Dynamic User Behavior: A Universal Solution (2023)

A practical barrier to the implementation of cache-aided networks is dynamic and unpredictable user behavior. In dynamic setups, users can freely depart and enter the network at any moment. The shared caching concept has the potential to handle this issue by assigning $K$ users to $P$ caching profiles, where all $η_{p}$ users assigned to profile $p$ store the same cache content defined by that profile. The existing schemes, however, cannot be applied in general and are not dynamic in the true sense as they put constraints on the transmitter-side spatial multiplexing gain $α$. Specifically, they work only if $α\leq \min_{p} η_{p}$ or $α\geq \hatη$, where in the latter case, $γ$ is the normalized cache size of each user, $\hatη$ is an arbitrary parameter satisfying $1 \leq \hatη \leq \max_{p} η_{p}$, and the extra condition of $α\geq Kγ$ should also be met. In this work, we propose a universal caching scheme based on the same shared-cache model that can be applied to any dynamic setup, extending the working region of existing schemes to networks with $\min_{p} η_{p} \leq α\leq \hatη$ and removing any other constraints of existing schemes. We also derive the closed-form expressions for the achievable degrees-of-freedom (DoF) of the proposed scheme and show that it achieves the optimal DoF for uniform user distributions. Notably, it is the first scheme to achieve the optimal DoF of $Kγ+α$ for networks with uniform user distribution, $α&gt; \hatη$, and non-integer $\fracα{\hatη}$, without imposing any other constraints. Finally, we use numerical simulations to assess how non-uniform user distribution impacts the DoF performance and illustrate that the proposed scheme provides a noticeable improvement over unicasting for uneven distributions.
Outcomes of patients with renal monoclonal immunoglobulin deposition disease (2016)

Recent reports suggest that deep hematologic responses to chemotherapy are associated with improved renal outcomes in monoclonal immunoglobulin deposition disease (MIDD). Here we describe the long term outcomes and identify prognostic factors after first line treatment of the largest reported series of patients with MIDD. Between March 1992 and December 2014, 88 patients with MIDD were seen at Mayo Clinic, MN. Renal responses were defined using criteria used for light chain amyloidosis (AL) or those used by the IMWG. Sixty-one (69%) patients had a GFR < 30 mL/min/1.73 m<sup>2</sup> and 16 (18%) were on renal replacement therapy at diagnosis. The interval between albuminuria or elevation in creatinine and MIDD diagnosis was 12 months suggesting a delay in diagnosis. Thirty-seven patients (42%) had at least a hematologic CR/VGPR. Fifty-three (60%) received an autologous stem cell transplant (ASCT) or proteasome inhibitor (PI)-based treatments. Patients receiving ASCT or PI-based therapies were more likely to achieve at least a hematologic CR/VGPR compared to those receiving other therapies: 66% vs 2%, p < 0.0001. Patients that achieved a hematologic CR were more likely to achieve a renal response (53% vs 24%, p = 0.001). Five year overall and renal survival for the entire cohort was 67% and 57%, respectively. In multivariate analyses, a baseline GFR < 20 mL/min/1.73 m<sup>2</sup> and a renal response (using AL or IMWG criteria) were independently predictive of progression to dialysis. This study confirms that deep hematologic responses, best achieved with ASCT or PI-based therapies, are a prerequisite to achieving renal responses. Am. J. Hematol. 91:1123-1128, 2016. © 2016 Wiley Periodicals, Inc.
Analysis of the Phthiocerol Dimycocerosate Locus ofMycobacterium tuberculosis (2001)

Among the few characterized genes that have products involved in the pathogenicity of Mycobacterium tuberculosis, the etiological agent of tuberculosis, are those of the phthiocerol dimycocerosate (DIM) locus. Genes involved in biosynthesis of these compounds are grouped on a 50-kilobase fragment of the chromosome containing 13 genes. Analysis of mRNA produced from this 50-kilobase fragment in the wild type strain showed that this region is subdivided into three transcriptional units. Biochemical characterization of five mutants with transposon insertions in this region demonstrated that (i) the complete DIM molecules are synthesized in the cytoplasm of M. tuberculosis before being translocated into the cell wall; (ii) the genes fadD26 and fadD28 are directly involved in their biosynthesis; and (iii) both the drrC and mmpL7 genes are necessary for the proper localization of DIMs. Insertional mutants unable to synthesize or translocate DIMs exhibit higher cell wall permeability and are more sensitive to detergent than the wild type strain, indicating for the first time that, in addition to being important virulence factors, extractable lipids of M. tuberculosis play a role in the cell envelope architecture and permeability. This function may represent one of the molecular mechanisms by which DIMs are involved in the virulence of M. tuberculosis.
A new brain perfusion imaging agent: [I-123]HIPDM:N,N,N'-trimethyl-N'-[2-hydroxy-3-methyl-5-iodobenzyl]-1,3-propanediamine. (1983)

Based on the pH-shift mechanism, a new brain imaging agent I-124 HIPDM (N,N,N'-trimethyl-N'-[2-hydroxy-3-methyl-5-[123I]iodobenzyl]-1,3-propanediamine ) has been developed. This agent can be prepared by a simple exchange reaction suitable for routine clinical use. The physicochemical parameters, partition coefficient vs. pH profile, and protein binding, as well as biodistribution in rats, were very similar to those of I-123 IMP (N-isopropyl-p-iodoamphetamine). High brain uptake was found in animals after i.v. injection. The brain radioactivity persists for at least 1 hr in rats and monkeys. Regional distribution in sections of rat brain appeared to reflect regional perfusion. In conjunction with single-photon emission tomography (SPECT), this agent may provide useful information on local cerebral perfusion in humans.
A microfluidic approach for studying microcolonization of Escherichia coli O157:H7 on leaf trichome‐mimicking surfaces under fluid shear stress (2022)

Escherichia coli O157:H7 have previously been associated with disease outbreaks associated with leafy green vegetables. However, the physical mechanisms that determine the spatial organization of bacteria onto leafy greens are still not clear. Microfluidics with embedded trichome-mimicking microposts were employed to investigate the role of shear flow and configuration of trichomes on E. coli O157:H7 microcolonization. We characterized the three-dimensional microcolonization of green fluorescent protein (GFP)-tagged E. coli O157:H7 using multiphoton fluorescence microscopy and compared their differences under static (no flow; incubated for 36 h at 37°C) and fluid shear conditions (750 nl/min for 36 h at 37°C). For micropatterned trichome arrays, we demonstrated that natural wax-mixed polydimethylsiloxane retains similar topographies and contact angles to the surface of trichome-bearing leafy greens. Our results showed that E. coli O157:H7 under fluid shear stress aligned their colonization parallel to the direction of flow. In a static condition, their colonization had no preferential alignment, with statistically similar angular distributions in all directions. In addition, depending on dimensions of the trichome arrays and flow conditions, different bacterial microcolonization patterns grew radially from initial attachment; they formed into filamentous structures and developed into bridges by surface hydrophobicity and flow-induced shear with a nutrient-rich medium. Collectively, these results demonstrate how the consequences of bacterial colonization in response to shear flow can affect pathogenic bacterial contamination of leafy greens and biofilm architectures.
Selectivity profile comparison for certain γ-butyrolactone and oxazolidinone-based ligands on a sigma 2 receptor over sigma 1: a molecular docking approach (2022)

Sigma receptors (σ<sub>1</sub> R and σ<sub>2</sub> R) are pharmacologically characterized membrane-bound receptors that bind a wide range of chemical compounds. Alzheimer's disease, traumatic brain injury, schizophrenia, and neuropathic pain have all been associated with abnormal σ<sub>2</sub> activity. The σ<sub>2</sub> receptor has recently been identified as a potential therapeutic target for inhibiting the formation of amyloid plaques. Numerous laboratories are now investigating the potential of σ<sub>2</sub> ligands. Small molecule discovery is the focus of current research, with the goal of using target-based action to treat a variety of illnesses and ailments. Functionalized γ-butyrolactone and oxazolidinone-based ligands, in particular, are pharmacologically important scaffolds in drug discovery research and have been thoroughly examined for σ<sub>2</sub> receptor efficacy. The purpose of this study was to evaluate the pharmacophoric features of different σ<sub>2</sub> receptor ligands using <i>in silico</i> techniques. This study used a library of 58 compounds having a γ-butyrolactone and oxazolidinone core. To investigate the binding characteristics of the ligands with the σ<sub>2</sub> receptor, a 3D homology model was developed. To understand the binding pattern of the γ-butyrolactone and oxazolidinone based ligands, molecular docking studies were performed on both σ<sub>1</sub> and σ<sub>2</sub> receptors. Furthermore, MM/GBSA binding energy calculations were used to confirm the binding of ligands on the σ<sub>2</sub> over σ<sub>1</sub> receptor. These <i>in silico</i> findings will aid in the discovery of selective σ<sub>2</sub> ligands with good pharmacophoric properties and potency in the future.
Energy transfer within pi-conjugated peptide heterostructures in aqueous environments (2023)

Nanostructures comprising Π-conjugated peptides for energy migration in aqueous environments are disclosed. Conductive material comprising these nanostructures, and supramolecular assemblies comprising covalently-bound electron donor-acceptor chromophores for photoinduced electron transfer also are disclosed.
SiC Avalanche Photodiodes and Photomultipliers for Ultraviolet and Solar‐Blind Light Detection (2009)

This chapter contains sections titled: Introduction Silicon carbide avalanche photodiodes Influence of defects in SiC substrate on device performance Silicon carbide photomultiplier Summary References
Securing interconnected PUF network with reconfigurability (2018)

Physical Unclonable Functions (PUFs) are known for their unclonability and light-weight design. Recent advancement in technology has significantly compromised the security of PUFs. Machine learning-based attacks have been proven to be able to construct numerical models that predict various types of PUFs with high accuracy with a small set of challenge-response pairs (CRPs). To address the problem, we present a reconfigurable interconnected PUF network (IPN) design that significantly strengthens the security and unclonability of strong PUFs. While the IPN structure itself provides high resilience against modeling attacks, the reconfiguration mechanism remaps the input-output mapping before an attacker could collect sufficient CRPs. Experimental results show that all tested state-of-the-art machine learning attack methods have prediction accuracy of around 50% on a single bit output of a reconfigurable IPN.
Spectrum occupancy in the 2.36&#x2013;2.4 GHZ band: Measurements and analysis (2010)

In this paper, we analyze spectrum occupancy of the 2.36-2.4 GHz band. Interest in this band has risen recently, as secondary allocation of this radio spectrum is being considered for body sensor network operation to offer wireless healthcare services. We present spectrum measurements conducted in the Eindhoven area, in the Netherlands, where the 2.36-2.4 GHz band is currently used for land mobile and amateur radio services. Our objective is to show the spectrum usage in this band, provide statistics for the received power of active transmissions and obtain their occupation time.
Distibuted Dense Numerical Linear Algebra Algorithms on massively parallel architectures: DPLASMA (2010)

Abstract—We present DPLASMA, a new project related to PLASMA, that operates in the distributed memory regime. It uses a new generic distributed Direct Acyclic Graph engine for high performance computing (DAGuE). Our work also takes advantage of some of the features of DAGuE, such as DAG representation that is independent of problem-size, overlapping of communication and computation, task prioritization, architecture-aware scheduling and management of micro-tasks on distributed architectures that feature heterogeneous many-core nodes. The originality of this engine is that it is capable of translating a sequential nested-loop code into a concise and synthetic format which it can be interpret and then execute in a distributed environment. We consider three common dense linear algebra algorithms, namely: Cholesky, LU and QR factorizations, to investigate their data driven expression and execution in a distributed system. We demonstrate from our preliminary results that our DAG-based approach has the potential to bridge the gap between the peak and the achieved performance that is characteristic in the stateof-the-art distributed numerical softwares on current and emerging architectures. Index Terms—Linear systems, parallel algorithms, scheduling and task partitioning
Resonance Raman spectroscopy of volatile organics -- Carbon tetrachloride (1994)

Volatile organic chemicals are a class of pollutants which are regulated at very low levels by the EPA. Consequently a need exists as a part of site remediation efforts within DOE to develop technologies which will allow for the in situ monitoring of these chemicals. Resonance Raman spectroscopy is a potential technique to accomplish this if the resonance enhancement is sufficiently high. Carbon tetrachloride was selected as a test case. Measurements under resonance conditions at 248 nm showed an enhancement factor of 2 {times} 10{sup 4}. Using this value an estimate of the sensitivity for both in situ and remote monitoring of CCl{sup 4} was made. It was concluded that resonance Raman could be used to detect these chemicals at levels of regulatory interest. Future effort directed towards the development of a suitable probe as well as a field-portable system would be desirable. Such effort could be directed towards the solution of a particular monitoring problem within a DOE waste remediation project. Once developed, however, it should be easily generalized to the analysis of other VOC`s in other environments.
Transcription Factor Expression in the Hypothalamo-Neurohypophyseal System of the Dehydrated Rat: Upregulation of Gonadotrophin Inducible Transcription Factor 1 mRNA Is Mediated by cAMP-Dependent Protein Kinase A (2007)

The supraoptic (SON) and paraventricular (PVN) nuclei of the hypothalamo-neurohypophyseal system (HNS) undergo a dramatic function-related plasticity during dehydration. We hypothesize that alterations in steady-state transcript levels might be partially responsible for this remodeling. In turn, regulation of transcript abundance might be mediated by transcription factors. We used microarrays to identify changes in the expression of mRNAs encoding transcription factors in response to water deprivation in the SON. We observed downregulation of 10 and upregulation of 28 transcription factor transcripts. For five of the upregulated mRNAs, namely gonadotropin inducible ovarian transcription factor 1 (Giot1), Giot2, cAMP-responsive element binding protein 3-like 1, CCAAT/enhancer binding protein beta, and activating transcription factor 4, in situ hybridization was used to confirm the array results, demonstrating a significant increase in expression in SON and PVN magnocellular neurons (MCNs) after 3 d of water deprivation and, in some cases, upregulation in parvocellular PVN neurons. Using a viral vector expressing a potent inhibitor of cAMP-dependent protein kinase A (PKA), we show that the osmotically induced increase in the abundance of transcripts encoding Giot1 is mediated in vivo by the PKA pathway. We thus suggest that signaling pathways activated by dehydration in MCNs mediate transcription factor gene activation, which, in turn, regulate target genes that mediate HNS remodeling.
Temperature dependent two-photon photoluminescence of CH3NH3PbBr3: structural phase and exciton to free carrier transition (2018)

The intrinsic photoluminescence emission properties of high-quality bulk crystals of CH3NH3PbBr3 under excitation by two-photon absorption at 810 nm are presented. A strongly non-monotonous wavelength shift of the two-photon photoluminescence with increasing temperature is observed, which can be associated with discrete transitions between several stable crystalline phases. Experimentally, both temperature (5 – 300 K) and excitation density are varied. At room temperature, a scaling of the photoluminescence with the 4th power of the excitation density is observed, in contrast to a quadratic behavior at cryogenic temperatures. We attribute this due to a transition from exciton gas to free charge carriers with a temperature increase.
Signal-adaptive switching of overlap ratio in audio transform coding (2016)

Contemporary perceptual audio coders, all of which apply the modified discrete cosine transform (MDCT), with an overlap ratio of 50%, for frequency-domain quantization, provide good coding quality even at low bit-rates. However, relatively long frames are required for acceptable low-rate performance also for quasi-stationary harmonic input, leading to increased algorithmic latency and reduced temporal coding resolution. This paper investigates the alternative approach of employing the extended lapped transform (ELT), with 75% overlap ratio, on such input. To maintain a high time resolution for coding of transient segments, the ELT definition is modified such that frame-wise switching between ELT (for quasi-stationary) and MDCT coding (for non-stationary or non-tonal regions), with complete time-domain aliasing cancelation and no increase in frame length, becomes possible. A new ELT window function with improved side-lobe rejection to avoid framing artifacts is also derived. Blind subjective evaluation of the switched-ratio proposal confirms the benefit of the signal-adaptive design.
Dielectric Charging in Electrostatically Actuated MEMS Ohmic Switches (2008)

MEMS switches having separate signal and actuation electrodes with different air gaps are fabricated using a copper-based CMOS interconnect manufacturing process. By using a control voltage high enough to establish metal-metal contact between the signal electrodes while avoiding contact between the dielectric-covered actuation electrodes, dielectric charging appears to be tolerable. By simultaneously measuring the conductance across the signal electrodes and the capacitance across the actuation electrodes, the conductance-force characteristic can be readily monitored and analyzed. For the present switches, the effect of polarization charge appears to be negligible, and dielectric charging is significant only after dielectric contact is made and space charge is injected.