gebhart/patrepeval huggingface dataset:
PCR-Based Approach Targeting Mucorales-Specific Gene Family for Diagnosis of Mucormycosis (2018)

Mucormycosis is an aggressive, life-threatening infection caused by fungi in the order Mucorales. The current diagnosis of mucormycosis relies on mycological cultures, radiology and histopathology. These methods lack sensitivity and are most definitive later in the course of infection, resulting in the prevention of timely intervention. PCR-based approaches have shown promising potential in rapidly diagnosing mucormycosis. The spore coating protein homolog encoding <i>CotH</i> genes are uniquely and universally present among Mucorales. Thus, <i>CotH</i> genes are potential targets for the rapid diagnosis of mucormycosis. We infected mice with different Mucorales known to cause human mucormycosis and investigated whether <i>CotH</i> could be PCR amplified from biological fluids. Uninfected mice and those with aspergillosis were used to determine the specificity of the assay. <i>CotH</i> was detected as early as 24 h postinfection in plasma, urine, and bronchoalveolar lavage (BAL) samples from mice infected intratracheally with <i>Rhizopus delemar</i>, <i>Rhizopus oryzae</i>, <i>Mucor circinelloides</i>, <i>Lichtheimia corymbifera</i>, or <i>Cunninghamella bertholletiae</i> but not from samples taken from uninfected mice or mice infected with <i>Aspergillus fumigatus</i> Detection of <i>CotH</i> from urine samples was more reliable than from plasma or BAL fluid. Using the receiver operating characteristic method, the sensitivity and the specificity of the assay were found to be 90 and 100%, respectively. Finally, <i>CotH</i> was PCR amplified from urine samples of patients with proven mucormycosis. Thus, PCR amplification of <i>CotH</i> is a promising target for the development of a reliable, sensitive, and simple method of early diagnosis of mucormycosis.
Reelin supplementation recovers sensorimotor gating, synaptic plasticity and associative learning deficits in the heterozygous reeler mouse (2012)

The lipoprotein receptor ligand Reelin is important for the processes of normal synaptic plasticity, dendritic morphogenesis, and learning and memory. Heterozygous reeler mice (HRM) show many neuroanatomical, biochemical, and behavioral features that are associated with schizophrenia. HRM show subtle morphological defects including reductions in dendritic spine density, altered synaptic plasticity and behavioral deficits in associative learning and memory and pre-pulse inhibition. The present studies test the hypothesis that in vivo elevation of Reelin levels can rescue synaptic and behavioral phenotypes associated with HRM. We demonstrate that a single in vivo injection of Reelin increases GAD67 expression and alters dendritic spine morphology. In parallel we observed enhancement of hippocampal synaptic function and associative learning and memory. Reelin supplementation also increases pre-pulse inhibition. These results suggest that characteristics of HRM, similar to those observed in schizophrenia, are sensitive to Reelin levels and can be modified with Reelin supplementation in male and female adults.
A retrospective correction filter for discrete-time adaptive control of nonmiminum-phase systems (2008)

We present a discrete-time adaptive control law that is effective for systems that are unstable, MIMO, and/or nonminimum phase. The adaptive control algorithm provides guidelines concerning the modeling information needed for implementation. This information includes a sufficient number of Markov parameters to capture the sign of the high-frequency gain as well as the nonminimum-phase zeros. No additional information about the poles or zeros need be known.We present numerical examples to illustrate the algorithm¿s effectiveness in handling nonminimum-phase zeros.
Synchronous Control of a Static AC Induction Motor Drive (1979)

Conventional methods of controlling an induction motor utilize regulation of stator current and motor slip frequency in order to maintain system stability. This control strategy requires a shaft speed feedback and fast-response current regulation. An alternative method of controlling an induction motor is presented which achieves the necessary system stabilization by controlling only the motor frequency. The control inherently regulates the motor torque angle by properly adjusting the phase of the converter firing signals. By synchronizing the inverter firing pulses to the motor back electromotive force (EMF) possible adverse inverter operating modes are avoided. The concept of synchronous control eliminates the preprogrammed functional relations previously required and allows the control to adapt to any desired motor flux level. Any desired outer regulating loop can be incorporated to form a fast-response wide-range ac drive system.
Identification of Unique Gene Expression Profile in Children with Regressive Autism Spectrum Disorder (ASD) and Ileocolitis (2013)

Gastrointestinal symptoms are common in children with autism spectrum disorder (ASD) and are often associated with mucosal inflammatory infiltrates of the small and large intestine. Although distinct histologic and immunohistochemical properties of this inflammatory infiltrate have been previously described in this ASD(GI) group, molecular characterization of these lesions has not been reported. In this study we utilize transcriptome profiling of gastrointestinal mucosal biopsy tissue from ASD(GI) children and three non-ASD control groups (Crohn's disease, ulcerative colitis, and histologically normal) in an effort to determine if there is a gene expression profile unique to the ASD(GI) group. Comparison of differentially expressed transcripts between the groups demonstrated that non-pathologic (normal) tissue segregated almost completely from inflamed tissue in all cases. Gene expression profiles in intestinal biopsy tissue from patients with Crohn's disease, ulcerative colitis, and ASD(GI), while having significant overlap with each other, also showed distinctive features for each group. Taken together, these results demonstrate that ASD(GI) children have a gastrointestinal mucosal molecular profile that overlaps significantly with known inflammatory bowel disease (IBD), yet has distinctive features that further supports the presence of an ASD-associated IBD variant, or, alternatively, a prodromal phase of typical inflammatory bowel disease. Although we report qPCR confirmation of representative differentially expressed transcripts determined initially by microarray, these findings may be considered preliminary to the extent that they require further confirmation in a validation cohort.
Development and Physical Characterization of α-Glucan Nanoparticles (2020)

α-Glucans that were enzymatically synthesized from sucrose using glucansucrase cloned from <i>Leuconostoc mesenteroides</i> NRRL B-1118 were found to have a glass transition temperature of approximately 80 °C. Using high-pressure homogenization (~70 MPa), the α-glucans were converted into nanoparticles of ~120 nm in diameter with a surface potential of ~-3 mV. Fluorescence measurements using 1,6-diphenyl-1,3,5-hexatriene (DPH) indicate that the α-glucan nanoparticles have a hydrophobic core that remains intact from 10 to 85 °C. α-Glucan nanoparticles were found to be stable for over 220 days and able to form at three pH levels. Accelerated exposure measurements demonstrated that the α-glucan nanoparticles can endure exposure to elevated temperatures up to 60 °C for 6 h intervals.
Selective Recapitulation of Conserved and Nonconserved Regions of Putative NOXA1 Protein Activation Domain Confers Isoform-specific Inhibition of Nox1 Oxidase and Attenuation of Endothelial Cell Migration (2013)

Excessive vascular and colon epithelial reactive oxygen species production by NADPH oxidase isoform 1 (Nox1) has been implicated in a number of disease states, including hypertension, atherosclerosis, and neoplasia. A peptide that mimics a putative activation domain of the Nox1 activator subunit NOXA1 (NOXA1 docking sequence, also known as NoxA1ds) potently inhibited Nox1-derived superoxide anion (O2·-) production in a reconstituted Nox1 cell-free system, with no effect on Nox2-, Nox4-, Nox5-, or xanthine oxidase-derived reactive oxygen species production as measured by cytochrome c reduction, Amplex Red fluorescence, and electron paramagnetic resonance. The ability of NoxA1ds to cross the plasma membrane was tested by confocal microscopy in a human colon cancer cell line exclusively expressing Nox1 (HT-29) using FITC-labeled NoxA1ds. NoxA1ds significantly inhibited whole HT-29 carcinoma cell-derived O2·- generation. ELISA and fluorescence recovery after photobleaching experiments indicate that NoxA1ds, but not its scrambled control, binds Nox1. FRET experiments conducted using Nox1-YFP and NOXA1-CFP illustrate that NoxA1ds disrupts the binding interaction between Nox1 and NOXA1, whereas a control peptide did not. Moreover, hypoxia-induced human pulmonary artery endothelial cell O2·- production was completely inhibited by NoxA1ds. Human pulmonary artery endothelial cell migration under hypoxic conditions was also reduced by pretreatment with NoxA1ds. Our data indicate that a peptide recapitulating a putative activation subdomain of NOXA1 (NoxA1ds) is a highly efficacious and selective inhibitor of Nox1 activity and establishes a critical interaction site for Nox1-NOXA1 binding required for enzyme activation.
Hybrid Electrolytes with Controlled Network Structures for Lithium Metal Batteries (2015)

Solid polymer electrolytes (SPEs) with tunable network structures are prepared by a facile one-pot reaction of polyhedral oligomeric silsesquioxane and poly(ethylene glycol). These SPEs, with high conductivity and high modulus, exhibit superior resistance to lithium dendrite growth even at high current densities. Measurements of lithium metal batteries with a LiFePO4 cathode show excellent cycling stability and rate capability.
Perfect Bi<sub>4</sub>Ti<sub>3</sub>O<sub>12</sub> Single‐Crystal Films via Flux‐Mediated Epitaxy (2006)

Abstract Excellent crystallinity of material films and atomic control of their surface/interface, sufficient for the realization of their optimal physical properties, are technological premises for modern functional‐device applications. Bi 4 Ti 3 O 12 and related compounds attract much interest as highly insulating, ferroelectric materials for use in ferroelectric random‐access memories. However, it has been difficult thus far for Bi 4 Ti 3 O 12 films to satisfy such requirements when formed using vapor‐phase epitaxy, owing to the high volatility of Bi in a vacuum. Here, we demonstrate that flux‐mediated epitaxy is one of the most promising and widely applicable concepts to overcome this inevitable problem. The key point of this process is the appropriate selection of a multi‐component flux system. A combinatorial approach has led to the successful discovery of the novel flux composition of Bi–Cu–O for Bi 4 Ti 3 O 12 single‐crystal film growth. The perfect single‐crystal nature of the stoichiometric Bi 4 Ti 3 O 12 film formed has been verified through its giant grain size and electric properties, equivalent to those of bulk single crystals. This demonstration has broad implications, opening up the possibility of preparing stoichiometric single‐crystal oxide films via vapor‐phase epitaxy, even if volatile constituents are required.
Inhibition of Francisella tularensis phagocytosis using a novel anti-LPS scFv antibody fragment (2019)

Francisella tularensis (Ft), the causative agent of lethal tularemia, is classified as a category A biological warfare threat agent. While Ft infection is treatable by antibiotics, many failed antibiotic treatments were reported, highlighting the need for effective new treatments. It has been demonstrated that binding of antibody-coated bacteria to the Fc receptor located on phagocytic cells is a key process needed for efficient protection against Ft. Yet, Ft utilizes the same receptor to enter the phagocytic cells in order to escape the immune system. To address the question whether an anti-Ft LPS antibody lacking the ability to bind the Fc receptor may inhibit the entry of Ft into host cells, a soluble scFv (TL1-scFv) was constructed from an anti Ft-LPS antibody (TL1) that was isolated from an immune single-chain (scFv) phage-display library. Bacterial uptake was assessed upon infection of macrophages with Ft live attenuated strain (LVS) in the presence of either TL1 or TL1-scFv. While incubation of LVS in the presence of TL1 greatly enhanced bacterial uptake, LVS uptake was significantly inhibited in the presence of TL1-scFv. These results prompt further experiments probing the therapeutic efficacy of TL1-scFv, alone or in combination with antibiotic treatment.
Detection of atrial fibrillation and other abnormal rhythms from ECG using a multi-layer classifier architecture (2019)

Further, the proposed algorithm has achieved joint first place in the PhysioNet/Computing in Cardiology Challenge 2017 with a score of 0.83 computed on a hidden test dataset.
Post-Tensioned Traffic Signal Structure: Experimental Natural Wind Response and Fatigue Assessment (2016)

Cantilevered traffic signal structures undergo wind-induced vibrations causing persistent stress cycles that result in welded connection fatigue and fracture. A low-cost damage avoidance concept is proposed to apply post-tensioned prestress to eradicate the detrimental tensile mean stresses found in the tube-to-transverse end plate welded connections. A supplementary load path is introduced to balance the moments arising from the significant dead load associated with the cantilevered arm spanning the roadway, while offering a fail-safe mechanism. Field observations are made on a full-scale prototype structure in a natural wind environment without and with the proposed mitigation system installed; changes in the structure’s stress response are monitored. To quantify the benefit of the proposed system, the fatigue life is estimated using a deterministic framework considering the expected change in fatigue resistance and observed changes in natural wind response for two contrasting wind environments. Test results and companion analyses show that there is potential to markedly extend the fatigue (service) life of the traffic signal structure of subject in this study well beyond its expected service life. The proposed concept shows potential to reduce detrimental tensile mean stress effects for a variety of fatigue-critical, lightweight steel infrastructure components.
PlayStation 3-based tele-rehabilitation for children with hemiplegia (2008)

The convergence of game technology (software and hardware), the Internet, and rehabilitation science forms the second-generation virtual rehabilitation framework. This reduced-cost and patient/therapist familiarity facilitate adoption in clinical practice. This paper presents a PlayStation 3-based hand physical rehabilitation system for children with hemiplegia due to perinatal brain injury (hemiplegic cerebral palsy) or later childhood stroke. Unlike precursor systems aimed at providing hand training for post-stroke adults in a clinical setting, the experimental system described here was developed for in-home tele-rehabilitation on a game console for children and adults with chronic hemiplegia after stroke or other focal brain injury. Significant improvements in Activities of Daily Living function followed three months of training at home on the system. Clinical trials are ongoing at this time.
Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions (2012)

We present novel homobifunctional amine-reactive clickable cross-linkers (CXLs) for investigation of three-dimensional protein structures and protein-protein interactions (PPIs). CXLs afford consolidated advantages not previously available in a simple cross-linker, including (1) their small size and cationic nature at physiological pH, resulting in good water solubility and cell-permeability, (2) an alkyne group for bio-orthogonal conjugation to affinity tags via the click reaction for enrichment of cross-linked peptides, (3) a nucleophilic displacement reaction involving the 1,2,3-triazole ring formed in the click reaction, yielding a lock-mass reporter ion for only clicked peptides, and (4) higher charge states of cross-linked peptides in the gas-phase for augmented electron transfer dissociation (ETD) yields. Ubiquitin, a lysine-abundant protein, is used as a model system to demonstrate structural studies using CXLs. To validate the sensitivity of our approach, biotin-azide labeling and subsequent enrichment of cross-linked peptides are performed for cross-linked ubiquitin digests mixed with yeast cell lysates. Cross-linked peptides are detected and identified by collision induced dissociation (CID) and ETD with linear quadrupole ion trap (LTQ)-Fourier transform ion cyclotron resonance (FTICR) and LTQ-Orbitrap mass spectrometers. The application of CXLs to more complex systems (e.g., in vivo cross-linking) is illustrated by Western blot detection of Cul1 complexes including known binders, Cand1 and Skp2, in HEK 293 cells, confirming good water solubility and cell-permeability.
Integrated optical gyroscope using active Long-range surface plasmon-polariton waveguide resonator (2014)

Optical gyroscopes with high sensitivity are important rotation sensors for inertial navigation systems. Here, we present the concept of integrated resonant optical gyroscope constructed by active long-range surface plasmon-polariton (LRSPP) waveguide resonator. In this gyroscope, LRSPP waveguide doped gain medium is pumped to compensate the propagation loss, which has lower pump noise than that of conventional optical waveguide. Peculiar properties of single-polarization of LRSPP waveguide have been found to significantly reduce the polarization error. The metal layer of LRSPP waveguide is electro-optical multiplexed for suppression of reciprocal noises. It shows a limited sensitivity of ~10−4 deg/h and a maximum zero drift which is 4 orders of magnitude lower than that constructed by conventional single-mode waveguide.
Minimization of CSI Feedback Dimension for Interference Alignment in MIMO Interference Multicast Networks (2015)

It is well-known that interference alignment (IA) can achieve substantial theoretical gains in multiple-input multiple-output (MIMO) networks. However, the conventional works usually assume the full channel state information (CSI) is available at the transmitter side, which would create a overwhelming CSI feedback overhead for practical frequency-division duplexing (FDD) wireless systems. To implement IA in practice, it is highly desirable to reduce the amount of required CSI feedback overhead. In this paper, we consider IA in MIMO interference multicast networks under partial CSI feedback, and we attempt to minimize the CSI feedback cost subject to IA feasibility constraints with a given degree of freedom (DoF) requirements. First, we propose a CSI feedback profile to embrace two important CSI feedback reduction strategies and we use the metric of CSI feedback dimension to quantify the associated CSI feedback cost. We then formulate the IA conditions under partial CSI feedback in MIMO interference multicast networks and we derive new IA feasibility conditions under the proposed partial CSI feedback framework. Based on these results, we consider the CSI feedback dimension minimization subject to the IA feasibility constraints with a given DoF requirements in MIMO interference multicast networks, which is formulated as a combinatorial optimization problem. Based on the specific problem structure, we derive an asymptotically optimal solution for a category of network topologies and we further obtain closed-form tradeoff results between DoFs and the CSI feedback cost for MIMO interference multicast networks.
Learning a multiscale patch-based representation for image denoising in X-RAY fluoroscopy (2016)

Denoising is an indispensable step in processing low-dose X-ray fluoroscopic images that requires development of specialized high-quality algorithms able to operate in near real-time. We address this problem with an efficient deep learning approach based on the process-centric view of traditional iterative thresholding methods. We develop a novel trainable patch-based multiscale framework for sparse image representation. In a computationally efficient way, it allows us to accurately reconstruct important image features on multiple levels of decomposition with patch dictionaries of reduced size and complexity. The flexibility of the chosen machine learning approach allows us to tailor the learned basis for preserving important structural information in the image and noticeably minimize the amount of artifacts. Our denoising results obtained with real clinical data demonstrate significant quality improvement and are computed much faster in comparison with the BM3D algorithm.
Latte: Large-Scale Lateral Movement Detection (2018)

The frequency of recent headlines indicates that attacks on governmental and corporate computer networks are increasing. Once they infect one computer, the attackers are quite likely to explore the network by accessing additional computers. Such “lateral movement”, i.e., the process attackers use to move from one computer to the next in a compromised network, increases the difficulties of preventing data exfiltration. To deal with challenges from large-scale data and little knowledge of the attackers, we propose Latte, a graph-based detection system to discover potential malicious lateral movement paths. We model computers and accounts as nodes, and computer-to-computer connections or user logon events as edges. We address the lateral movement problem in two ways. Starting with an infected computer or account, forensic analysis quickly identifies other compromised computers. To discover a new attack, general detection identifies unknown lateral movement across nodes which are not known to be compromised. A key component for general detection is a remote file execution detector which filters out the majority of the rare paths in the network. We provide separate algorithms for these subproblems and validate their effectiveness and efficiency on two, large-scale datasets, including one with a confirmed attack and one from a penetration test.
High-Power Higher Order Hermite–Gaussian and Laguerre–Gaussian Beams From Vertical External Cavity Surface Emitting Lasers (2019)

We report a vertical external cavity surface emitting laser (VECSEL) with an optical pumping scheme for the generation of higher order Hermite-Gaussian transverse modes. The VECSEL chip with emission around 1068 nm in a linear cavity configuration is capable of delivering a variety of higher order modes with Watt-level output power. A very good agreement between the modeling and experimental results validate the ideas underpinning the method. Additionally, simultaneous lasing of two independent and collinear transverse modes from a single laser cavity is demonstrated. An external astigmatic mode converter is finally utilized for the conversion of Hermite-Gaussian modes into corresponding Laguerre-Gaussian modes.