gebhart/patrepeval huggingface dataset:
Joint Optimization of Masks and Deep Recurrent Neural Networks for Monaural Source Separation (2015)

Monaural source separation is important for many real world applications. It is challenging because, with only a single channel of information available, without any constraints, an infinite number of solutions are possible. In this paper, we explore joint optimization of masking functions and deep recurrent neural networks for monaural source separation tasks, including speech separation, singing voice separation, and speech denoising. The joint optimization of the deep recurrent neural networks with an extra masking layer enforces a reconstruction constraint. Moreover, we explore a discriminative criterion for training neural networks to further enhance the separation performance. We evaluate the proposed system on the TSP, MIR-1K, and TIMIT datasets for speech separation, singing voice separation, and speech denoising tasks, respectively. Our approaches achieve 2.30-4.98 dB SDR gain compared to NMF models in the speech separation task, 2.30-2.48 dB GNSDR gain and 4.32-5.42 dB GSIR gain compared to existing models in the singing voice separation task, and outperform NMF and DNN baselines in the speech denoising task.
A case report of metastatic male breast cancer from renal cell carcinoma (2013)

症例は75歳，男性で，2008年に左腎細胞癌（T1bN0M0）で左腎摘除術を受けている．病理診断はrenal cell carcinoma（clear cell carcinoma）であった．術後3年目のfollow up CTで，左乳房内に径7mmの高濃度結節を認めた．さらに，半年後のCTでは径13mmと増大傾向を認めた．USは左乳房CD領域に境界明瞭で，内部血流の豊富な低エコー腫瘤を認め，針生検で腎癌と類似した組織像を認め，renal cell carcinomaの乳腺転移と診断した．男性の原発性乳癌は全乳癌の1％程度であるが，転移性乳癌はさらに稀少である．また，転移性乳癌の原発巣は本邦では対側乳癌，胃癌，白血病，悪性リンパ腫の順に多いが，腎癌からの乳腺転移はほとんど報告例をみない．今回我々は，男性で腎癌の乳腺転移と診断した非常にまれな症例を経験したので，若干の文献的考察を加えて報告する．
Vpr R77Q is associated with long-term nonprogressive HIV infection and impaired induction of apoptosis (2003)

The absence of immune defects that occurs in the syndrome of long-term nonprogressive (LTNP) HIV infection offers insights into the pathophysiology of HIV-induced immune disease. The (H[F/S]RIG) 2 domain of viral protein R (Vpr) induces apoptosis and may contribute to HIV-induced T cell depletion. We demonstrate a higher frequency of R77Q Vpr mutations in patients with LTNP than in patients with progressive disease. In addition, T cell infections using vesicular stomatitis virus G (VSV-G) pseudotyped HIV-1 Vpr R77Q result in less (P = 0.01) T cell death than infections using wild-type Vpr, despite similar levels of viral replication. Wild-type Vpr-associated events, including procaspase-8 and -3 cleavage, loss of mitochondrial transmembrane potential ( m ), and DNA fragmentation factor activation are attenuated by R77Q Vpr. These data highlight the pathophysiologic role of Vpr in HIV-induced immune disease and suggest a novel mechanism of LTNP.
A New Era of Image Guidance with Magnetic Resonance-guided Radiation Therapy for Abdominal and Thoracic Malignancies (2018)

Magnetic resonance-guided radiation therapy (MRgRT) offers advantages for image guidance for radiotherapy treatments as compared to conventional computed tomography (CT)-based modalities. The superior soft tissue contrast of magnetic resonance (MR) enables an improved visualization of the gross tumor and adjacent normal tissues in the treatment of abdominal and thoracic malignancies. Online adaptive capabilities, coupled with advanced motion management of real-time tracking of the tumor, directly allow for high-precision inter-/intrafraction localization. The primary aim of this case series is to describe MR-based interventions for localizing targets not well-visualized with conventional image-guided technologies. The abdominal and thoracic sites of the lung, kidney, liver, and gastric targets are described to illustrate the technological advancement of MR-guidance in radiotherapy.
The kappa opioid agonist GR89 696 blocks hyperalgesia and allodynia in rat models of peripheral neuritis and neuropathy (1999)

Previous work demonstrated that, in rats, intrathecal GR89696, a putative kappa-2 opioid receptor agonist, inhibited hyperalgesia to noxious heat in an inflamed hind paw (anti-hyperalgesic effect). Non-inflamed paws were not influenced by kappa-2 receptor activation. The question addressed in this study was whether GR89696 was as effective in blocking hyperalgesia and allodynia in nerve injury models as it was in the inflammation model. GR89696 (6 nmoles, i.t.) completely reversed the hyperalgesia and allodynia observed in both the neuropathy and neuritis models in all sensory tests. However, it did not alter sensory function in non-injured limbs nor in sham operated animals. Naloxone (1 mg/kg, i.p.) reversed the anti-hyperalgesic and anti-allodynic effects of GR89696. The mu agonist DAMGO (6 nmoles, i.t.) and the kappa-1 agonist U69593 (100 nmoles, i.t.) only partially reversed hyperalgesia and allodynia. These findings suggest that kappa-2 opioid receptors may be a useful target for the pharmacological control of hyperalgesia and allodynia.
Optimal “image‐based” weighting for energy‐resolved CT (2009)

This paper investigates a method of reconstructing images from energy-resolved CT data with negligible beam-hardening artifacts and improved contrast-to-nosie ratio (CNR) compared to conventional energy-weighting methods. Conceptually, the investigated method first reconstructs separate images from each energy bin. The final image is a linear combination of the energy-bin images, with the weights chosen to maximize the CNR in the final image. The optimal weight of a particular energy-bin image is derived to be proportional to the contrast-to-noise-variance ratio in that image. The investigated weighting method is referred to as "image-based" weighting, although, as will be described, the weights can be calculated and the energy-bin data combined prior to reconstruction. The performance of optimal image-based energy weighting with respect to CNR and beam-hardening artifacts was investigated through simulations and compared to that of energy integrating, photon counting, and previously studied optimal "projection-based" energy weighting. Two acquisitions were simulated: dedicated breast CT and a conventional thorax scan. The energy-resolving detector was simulated with five energy bins. Four methods of estimating the optimal weights were investigated, including task-specific and task-independent methods and methods that require a single reconstruction versus multiple reconstructions. Results demonstrated that optimal image-based weighting improved the CNR compared to energy-integrating weighting by factors of 1.15-1.6 depending on the task. Compared to photon-counting weighting, the CNR improvement ranged from 1.0 to 1.3. The CNR improvement factors were comparable to those of projection-based optimal energy weighting. The beam-hardening cupping artifact increased from 5.2% for energy-integrating weighting to 12.8% for optimal projection-based weighting, while optimal image-based weighting reduced the cupping to 0.6%. Overall, optimal image-based energy weighting provides images with negligible beam-hardening artifacts and improved CNR compared to energy-integrating and photon-counting methods.
Design and Optimization of Pyrazinecarboxamide-Based Inhibitors of Diacylglycerol Acyltransferase 1 (DGAT1) Leading to a Clinical Candidate Dimethylpyrazinecarboxamide Phenylcyclohexylacetic Acid (AZD7687) (2012)

A new series of pyrazinecarboxamide DGAT1 inhibitors was designed to address the need for a candidate drug with good potency, selectivity, and physical and DMPK properties combined with a low predicted dose in man. Rational design and optimization of this series led to the discovery of compound 30 (AZD7687), which met the project objectives for potency, selectivity, in particular over ACAT1, solubility, and preclinical PK profiles. This compound showed the anticipated excellent pharmacokinetic properties in human volunteers.
Immunological targeting of tumor cells undergoing an epithelial-mesenchymal transition via a recombinant brachyury-yeast vaccine (2013)

The embryonic T-box transcription factor brachyury is aberrantly expressed in a range of human tumors. Previous studies have demonstrated that brachyury is a driver of the epithelial-mesenchymal transition (EMT), a process associated with cancer progression. Brachyury expression in human tumor cells enhances tumor invasiveness in vitro and metastasis in vivo, and induces resistance to various conventional therapeutics including chemotherapy and radiation. These characteristics, and the selective expression of brachyury for a range of human tumor types vs. normal adult tissues, make brachyury an attractive tumor target. Due to its intracellular localization and the "undruggable" character of transcription factors, available options to target brachyury are currently limited. Here we report on the development and characterization of an immunological platform for the efficient targeting of brachyury-positive tumors consisting of a heat-killed, recombinant Saccharomyces cerevisiae (yeast)-brachyury vector-based vaccine (designated as GI-6301) that expresses the full-length human brachyury protein. We demonstrate that human dendritic cells treated with recombinant yeast-brachyury can activate and expand brachyury-specific CD4+ and CD8+ T cells in vitro that, in turn, can effectively lyse human tumor cells expressing the brachyury protein. Vaccination of mice with recombinant yeast-brachyury is also shown here to elicit brachyury-specific CD4+ and CD8+ T-cell responses, and to induce anti-tumor immunity in the absence of toxicity. Based on these results, a Phase I clinical trial of GI-6301 is currently ongoing in patients with advanced tumors; to our knowledge, this is the first vaccine platform aimed at targeting a driver of tumor EMT that has successfully reached the clinical stage.
Blockage of chemotactic peptide-induced stimulation of neutrophils by wortmannin as a result of selective inhibition of phosphatidylinositol 3-kinase. (1994)

Wortmannin, a fungal metabolite, inhibited 32P labeling of phosphatidylinositol trisphosphate, a product of phosphatidylinositol 3-kinase (PI 3-kinase), selectively in formyl peptide-stimulated 32P-loaded guinea pig neutrophils. The inhibition was of the same concentration dependence (with the half-maximal inhibition around 50 nM) as was observed for the simultaneous inhibition of formyl peptide-induced superoxide anion production. Wortmannin inhibited all three of the PI 3-kinase activities found in the cytosol fraction of guinea pig neutrophils, with a similar dose dependence (the half-maximal effects at 5 nM). Wortmannin was also effective on an immunologically purified preparation of the enzyme. The inhibition was of a noncompetitive type with regard to ATP and was observed consistently when PI, PI monophosphate, or PI bisphosphate was used as substrate. PI 4-kinase activity was not affected. It is concluded, therefore, that wortmannin abolished the formyl peptide-induced stimulation of neutrophils as a result of the inhibition of PI 3-kinase. An essential role of PI 3-kinase in receptor-mediated signaling in neutrophils thus evidenced with the use of wortmannin will be expanded to other cellular signaling systems.
FPGA-based Internet protocol firewall chip (2002)

We present the design of a firewall for IP networks using a field-programmable gate array (FPGA). The FPGA implements, in hardware, the accept or deny rules of the firewall. A hardware-based firewall offers the advantages of speed over a software firewall, in addition to direct interfacing with network devices, such as an Ethernet or a serial line transceiver. This paper shows how the rules are translated to VHDL and then implemented in hardware, and how the hardware is utilized to filter network traffic in a packet-by-packet fashion, or based on connection information, with a speed of more than 500,000 packets per second.
THE EFFECT OF SCARIFICATION ON ARTICULAR CARTILAGE IN THE RABBIT (1963)

1. The changes resulting from superficial scarification of articular cartilage have been observed in the knee joint of adult rabbits. A reduction in the amount of stainable matrix ground substance occurred at the sites of damage. Particular attention was therefore paid to sulphated mucopolysaccharide synthesis by cartilage cells in or near the traumatised areas. 2. The femoral groove cartilage one week after scarification showed evidence of increased mucopolysaccharide synthesis, especially by the more superficial chondrocytes near the cuts, but three or four weeks later the enhanced chondrocyte activity tended to diminish, and after six weeks the superficial cells near the cuts were found to be inactive. From six to thirty-four weeks the loss of stainable ground substance extended more deeply, but cell degeneration in these deeper areas of matrix depletion was preceded by a period in which many of the deeper chondrocytes still showed evidence of active mucopolysaccharide synthesis. Cellular activity in tags of depleted cartilage was usually lost before the tags finally disintegrated. Chondrocyte clusters were often seen in the scarified areas, especially in the deeper zones. They seemed to be a reactive rather than degenerative phenomenon. 3. In the scarified cartilages of the patella examined after one week a reactive response by superficial chondrocytes was less evident than in the femoral cartilage from the same joint, and after six weeks areas of deeply extending matrix loss were exceptional. 4. The structural and functional changes in the rabbits' femoral articular cartilage after its scarification resembled those which have been observed in the developing cartilage lesion of human osteoarthritis–namely, loss of interstitial matrix and superficial fibrillation, a stimulated synthesis of chondroitin sulphate by the chondrocytes, and the appearance of cell clusters in the deeper zones. Within the period of the experiment, up to thirty-four weeks, the joint lesions remained strictly localised to the traumatised areas ofcartilage, and exposure of bone and joint remodelling, which are features of advanced osteoarthritis in man, were not seen.
Thermal Transport Measurements of Individual Multiwalled Nanotubes (2001)

The thermal conductivity and thermoelectric power of a single carbon nanotube were measured using a microfabricated suspended device. The observed thermal conductivity is more than 3000 W/K m at room temperature, which is 2 orders of magnitude higher than the estimation from previous experiments that used macroscopic mat samples. The temperature dependence of the thermal conductivity of nanotubes exhibits a peak at 320 K due to the onset of umklapp phonon scattering. The measured thermoelectric power shows linear temperature dependence with a value of 80 microV/K at room temperature.
Motion of transfer RNA from the A/T state into the A‐site using docking and simulations (2012)

The ribosome catalyzes peptidyl transfer reactions at the growing nascent polypeptide chain. Here, we present a structural mechanism for selecting cognate over near-cognate A/T transfer RNA (tRNA). In part, the structural basis for the fidelity of translation relies on accommodation to filter cognate from near-cognate tRNAs. To examine the assembly of tRNAs within the ribonucleic-riboprotein complex, we conducted a series of all-atom molecular dynamics (MD) simulations of the entire solvated 70S Escherichia coli ribosome, along with its associated cofactors, proteins, and messenger RNA (mRNA). We measured the motion of the A/T state of tRNA between initial binding and full accommodation. The mechanism of rejection was investigated. Using novel in-house algorithms, we determined trajectory pathways. Despite the large intersubunit cavity, the available space is limited by the presence of the tRNA, which is equally large. This article describes a "structural gate," formed between helices 71 and 92 on the ribosomal large subunit, which restricts tRNA motion. The gate and the interacting protein, L14, of the 50S ribosome act as steric filters in two consecutive substeps during accommodation, each requiring: (1) sufficient energy contained in the hybrid tRNA kink and (2) sufficient energy in the Watson-Crick base pairing of the codon-anticodon. We show that these barriers act to filter out near-cognate tRNA and promote proofreading of the codon-anticodon. Since proofreading is essential for understanding the fidelity of translation, our model for the dynamics of this process has substantial biomedical implications.
The Airway Epithelium as Immune Modulator (2003)

Keywords: airway epithelial cell, AEC; dendritic cell, DC; diesel exhaust particle, DEP; granulocyte–macrophage colony-stimulating factor, GM-CSF; human bronchial epithelial cells, HBEC; interleukin, IL; particulate matter, PM
Successful streptokinase therapy for catheter-induced subclavian vein thrombosis. (1980)

Synotinatuc subclavian vein thrombosis developed in a patient receiving long-term parenteral nutrition. Serial phlebograms showed progression of venous thrombosis, despite therapy with heparin. Fibrinolytic therapy with streptoikinase, monitored in the laboratory by the euglobulin clot lysis time, was strikingly successful and may be the treatment of choice for this condition if certain contraindications are absent.
Repaglinide/troglitazone combination therapy: improved glycemic control in type 2 diabetes. (2000)

Combination therapy with repaglinide and troglitazone leads to better glycemic control than monotherapy with either agent alone. Repaglinide monotherapy was more effective in lowering HbA1c levels than troglitazone monotherapy Repaglinide/troglitazone combination therapy was effective and did not show unexpected adverse events.
STAB‐SD: a Shine–Dalgarno sequence in the 5′ untranslated region is a determinant of mRNA stability (1996)

Transcription of the Bacillus thuringiensis cryIIIA toxin gene is initiated at nucleotide position -558 (relative to the cryIIIA start codon). However, the major cryIIIA transcript is an mRNA with its 5' end at nucleotide position -129. Fusions to the lacZ reporter gene revealed that the cryIIIA 5' untranslated region downstream of nucleotide position -129 acts as a 5' mRNA stabilizer. Deletion and mutation analysis suggest that the determinant of stability is a Shine-Dalgarno (SD) sequence close to the 5' end of the stable transcript. This SD sequence, designated STAB-SD, does not direct translation initiation. However, mutations predicted to weaken the putative interaction between the SD sequence and the 3' end of 16S rRNA lead to reduced mRNA stability. The binding of a 30S subunit to STAB-SD may be required for stabilization of cryIIIA mRNA as a transcript with a 5' end at nucleotide position -129. Similar STAB-SD sequences are found in the 5' untranslated regions of other cryIII genes, and in the 5' untranslated regions of genes from Gram-positive bacteria other than B. thuringiensis and may therefore be a widespread determinant of mRNA stability.
Fixed-lag Sampling Strategies for Particle Filtering SLAM (2007)

We describe two new sampling strategies for Rao-Blackwellized particle filtering SLAM. The strategies, called fixed-lag roughening and the block proposal distribution, both exploit "future" information, when it becomes available, to improve the filter's estimation for previous time steps. Fixed-lag roughening perturbs trajectory samples over a fixed lag time according to a Markov chain-Monte Carlo kernel. The block proposal distribution directly samples poses over a fixed lag from their fully joint distribution conditioned on all the available data. Our experimental results indicate that the proposed strategies, especially the block proposal, yield significant improvements in filter consistency and a reduction in particle degeneracies compared to standard sampling techniques such as the improved proposal distribution of FastSLAM 2.
The effects of intravenous angiotensin II upon blood pressure and sodium and urate excretion in human pregnancy (1988)

Twelve women in their first 3 months of pregnancy received an i.v. saline load (3 mmol sodium/kg) and a graded infusion of angiotensin II (Ang II; i.e. 4, 8 and 16 ng/kg per min). As controls, twelve comparable pregnant subjects received the saline infusion alone. Eight non-pregnant women underwent both protocols, with doses of 2, 4 and 8 ng/kg per min Ang II, and thus acted as their own controls. Saline loading evoked proportionately similar falls in basal plasma renin (PRC) and plasma aldosterone (PAC) concentrations in pregnant and non-pregnant women. Angiotensin II evoked a dose-dependent pressor response, a graded increase in PAC and a reduction in sodium and urate excretion in both pregnant and non-pregnant women. The administration of Ang II had a proportionately greater effect on sodium and urate excretion in non-pregnant than in pregnant women; the pressor response to Ang II was also decreased in the pregnant women. The stimulation of PAC by Ang II, however, did not differ between the two groups. These results show that refractoriness to the renal and vascular effects of Ang II is present as early as the eleventh week of gestation. They also support the hypothesis that there is a degree of dissociation between the renin-angiotensin system and PAC in normal pregnancy.
Increasing Deep Neural Network Acoustic Model Size for Large Vocabulary Continuous Speech Recognition (2014)

Deep neural networks (DNNs) are now a central component of nearly all state-of-the-art speech recognition systems. Part of the promise of DNNs is their ability to represent increas-ingly complex functions as the number of DNN parameters increases. This paper investigates the performance of DNN-based hybrid speech recognition systems as DNN model size and training data increase. Using a distributed GPU architec-ture, we train DNN acoustic models roughly an order of mag-nitude larger than those typically found in speech recognition systems. DNNs of this scale achieve substantial reductions in final system word error rate despite training with a loss func-tion not tightly coupled to system error rate. However, training word error rate improvements do not translate to large improve-ments in test set word error rate for systems trained on the 300 hour Switchboard conversational speech corpus. Scaling DNN acoustic model size does prove beneficial on the Fisher 2,000 hour conversational speech corpus. Our results show that with sufficient training data, increasing DNN model size is an effec-tive, direct path to performance improvements. Moreover, even smaller DNNs benefit from a larger training corpus. Index Terms: speech recognition, neural networks, acoustic modeling
Detection of enterovirus and hepatitis A virus RNA in mussels (Mytilusspp.) by reverse transcriptase-polymerase chain reaction (2001)

The described method is effective for the detection of enteric viruses in mussels by RT-PCR. The use of Purescripttrade mark RNA isolation makes the method faster, safer and very easy to perform.
Glanders: an overview of infection in humans (2013)

Glanders is a highly contagious and often fatal zoonotic disease, primarily of solipds. In the developed world, glanders has been eradicated. However, prior use of B. mallei as a biological weapon and its high mortality in inhalation animal studies has affirmed B. mallei as a biodefense concern. This threat requires the development of new glanders medical countermeasures (MCMs), as there is a lack of an effective vaccine and lengthy courses of multiple antibiotics needed to eradicate B. mallei. Here, we present a literature review of human glanders in which we discuss the clinical epidemiology and risk factors, potential routes of exposure, symptoms, the incubation period, and specific diagnostics. This review focuses on pulmonary glanders, as this is the most likely outcome of a biological weapons attack. Additionally, we outline current treatment regimens and propose a clinical definition of human pulmonary glanders infection.