gebhart/patrepeval huggingface dataset:
MicroRNA-Regulated Pathways Associated with Endometriosis (2008)

Endometriosis is a prevalent gynecological disease characterized by growth of endometriotic tissue outside the uterine cavity. MicroRNAs (miRNAs) are naturally occurring posttranscriptional regulatory molecules that potentially play a role in endometriotic lesion development. We assessed miRNA expression by microarray analysis in paired ectopic and eutopic endometrial tissues and identified 14 up-regulated (miR-145, miR-143, miR-99a, miR-99b, miR-126, miR-100, miR-125b, miR-150, miR-125a, miR-223, miR-194, miR-365, miR-29c and miR-1) and eight down-regulated (miR-200a, miR-141, miR-200b, miR-142-3p, miR-424, miR-34c, miR-20a and miR-196b) miRNAs. The differential expression of six miRNAs was confirmed by quantitative RT-PCR. An in silico analysis identified 3851 mRNA transcripts as putative targets of the 22 miRNAs. Of these predicted targets, 673 were also differentially expressed in ectopic vs. eutopic endometrial tissue, as determined by microarray. Functional analysis suggested that the 673 miRNA targets constitute molecular pathways previously associated with endometriosis, including c-Jun, CREB-binding protein, protein kinase B (Akt), and cyclin D1 (CCND1) signaling. These pathways appeared to be regulated both transcriptionally as well as by miRNAs at posttranscriptional level. These data are a rich and novel resource for endometriosis and miRNA research and suggest that the 22 miRNAs and their cognate mRNA target sequences constitute pathways that promote endometriosis. Accordingly, miRNAs are potential therapeutic targets for treating this disease.
Walking in simulated reduced gravity: mechanical energy fluctuations and exchange (1999)

Walking humans conserve mechanical and, presumably, metabolic energy with an inverted pendulum-like exchange of gravitational potential energy and horizontal kinetic energy. Walking in simulated reduced gravity involves a relatively high metabolic cost, suggesting that the inverted-pendulum mechanism is disrupted because of a mismatch of potential and kinetic energy. We tested this hypothesis by measuring the fluctuations and exchange of mechanical energy of the center of mass at different combinations of velocity and simulated reduced gravity. Subjects walked with smaller fluctuations in horizontal velocity in lower gravity, such that the ratio of horizontal kinetic to gravitational potential energy fluctuations remained constant over a fourfold change in gravity. The amount of exchange, or percent recovery, at 1.00 m/s was not significantly different at 1.00, 0.75, and 0.50 G (average 64.4%), although it decreased to 48% at 0.25 G. As a result, the amount of work performed on the center of mass does not explain the relatively high metabolic cost of walking in simulated reduced gravity.
Schottky Solar Cells Based on Colloidal Nanocrystal Films (2008)

We describe here a simple, all-inorganic metal/NC/metal sandwich photovoltaic (PV) cell that produces an exceptionally large short-circuit photocurrent (>21 mA cm(-2)) by way of a Schottky junction at the negative electrode. The PV cell consists of a PbSe NC film, deposited via layer-by-layer (LbL) dip coating that yields an EQE of 55-65% in the visible and up to 25% in the infrared region of the solar spectrum, with a spectrally corrected AM1.5G power conversion efficiency of 2.1%. This NC device produces one of the largest short-circuit currents of any nanostructured solar cell, without the need for sintering, superlattice order or separate phases for electron and hole transport.
Impersonal mechanisms and personal networks in the distribution of grants in Japan (2001)

This paper shows that the distribution of grants to local governments is not significantly affected by individual political influence. Statistical analysis shows no link between the allocation of construction funds, for example, and the power of individual politicians. Instead, the distribution of such grants has tended to be stable across prefectures over time, indicating that bureaucratic formulae and historically determined entitlements dominate the distribution process.
The MUC1 Oncoprotein Activates the Anti-apoptotic Phosphoinositide 3-Kinase/Akt and Bcl-xL Pathways in Rat 3Y1 Fibroblasts (2004)

The MUC1 transmembrane glycoprotein is overexpressed by most human carcinomas. Overexpression of MUC1 confers transformation; however, the signaling pathways activated by this oncoprotein are largely unknown. The present studies demonstrated that MUC1-induced transformation of 3Y1 fibroblasts is associated with increased levels of phospho-Akt and phospho-Bad. The finding that LY294002 blocks MUC1-mediated increases in phospho-Akt and phospho-Bad supports the involvement of phosphoinositide 3-kinase (PI3K) as an upstream effector of this response. We also show that MUC1 increases the expression of the anti-apoptotic Bcl-x(L) protein (but not Bcl-2) by a PI3K-independent mechanism. In concert with these results, MUC1 attenuated (i) the loss of mitochondrial transmembrane potential, (ii) mitochondrial cytochrome c release, (iii) activation of caspase-9, and (iv) induction of apoptosis by the antimetabolite, 1-beta-d-arabinofuranosylcytosine. Similar results were obtained with the anti-cancer agent, gemcitabine. These findings indicate that expression of MUC1 in 3Y1 cells activates the anti-apoptotic PI3K/Akt and Bcl-x(L) pathways.
Calibration and basic motion of a micro hand module (2002)

A dexterous micro-manipulation system is developed for application in assembling micro-machine, manipulating cells, and micro-surgery. We have proposed a concept of a two finger micro-hand, and designed and built a hand module based on parallel mechanisms. The module has 6 degrees of freedom with piezoelectric devices as actuators. A calibration method based on least square error is proposed for 3-DOF translational motion in task coordinates fixed under a microscope. Coordinated motion is generated by both programming control and joystick teleoperation control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunohistochemical determination of in vivo distribution of Bax, a dominant inhibitor of Bcl-2. (1994)

The protein encoded by the bcl-2 gene is a regulator of programmed cell death and apoptosis. The cell survival-promoting activity of this protein is opposed by Bax, a homologous protein that forms heterodimers with Bcl-2 and accelerates rates of cell death. In this report, the in vivo patterns of bax gene expression were immunohistochemically assessed in the mouse, with a polyclonal antibody raised against a synthetic peptide corresponding to a unique region in the murine Bax protein. Direct comparisons were made with Bcl-2 by using anti-peptide antisera specific for the mouse Bcl-2 protein. The expression of bax was more widespread than bcl-2. For example, Bax immunoreactivity was present in the hepatocytes of the liver, the exocrine pancreas, and the renal tubule epithelial cells whereas Bcl-2 was absent from these tissues. Both the Bax and Bcl-2 proteins were present in several epithelia examined, including the small intestines, colon, breast, prostate, respiratory tract, and skin. The most intense Bax immunostaining was seen in cells located in the base of the crypts of the small intestinal mucosa, consistent with reports of high rates of spontaneous and inducible apoptosis in this region. Bcl-2 immunostaining was completely absent from these cells but was present in the absorptive epithelial cells of the small intestine. In contrast, Bax immunostaining in the colon tended to be stronger in the surface epithelial cells that had advanced up the crypts towards the lumen and that are destined for programmed cell death, whereas Bcl-2 immunoreactivity generally was stronger in the base of the colonic crypts. Similarly, bax expression in the gastric pits of the stomach occurred in a gradient such that higher levels of Bax immunostaining were found in the upper layers of gastric glands than in the lower regions. In addition, strong Bax immunostaining was detected in the androgen-dependent secretory epithelial cells of the prostate, whereas Bcl-2 was limited to the androgen-independent basal cells. Like Bcl-2, Bax was found in the thymic medulla but not the cortex, despite the propensity for immature cortical thymocytes to undergo apoptosis. Unlike Bcl-2, however, Bax immunostaining tended to be more intense in the germinal center lymphocytes of lymph nodes than in the interfollicular lymphocytes, consistent with the high rate of apoptotic cell death in the former.(ABSTRACT TRUNCATED AT 400 WORDS)
Mutagenesis of the putative fusion domain of the Semliki Forest virus spike protein (1991)

Semliki Forest virus (SFV), an alphavirus, infects cells via a low pH-triggered membrane fusion reaction that takes place within the cellular endocytic pathway. Fusion is mediated by the heterotrimeric virus spike protein, which undergoes conformational changes upon exposure to low pH. The SFV E1 spike subunit contains a hydrophobic domain of 23 amino acids that is highly conserved among alphaviruses. This region is also homologous to a domain of the rotavirus outer capsid protein VP4. Mutagenesis of an SFV spike protein cDNA was used to evaluate the role of the E1 domain in membrane fusion. Mutant spike proteins were expressed in COS cells and assayed for cell-cell fusion activity. Four mutant phenotypes were identified: (i) substitution of Gln for Lys-79 or Leu for Met-88 had no effect on spike protein fusion activity; (ii) substitution of Ala for Asp-75, Ala for Gly-83, or Ala for Gly-91 shifted the pH threshold of fusion to a more acidic range; (iii) mutation of Pro-86 to Asp, Gly-91 to Pro, or deletion of amino acids 83 to 92 resulted in retention of the E1 subunit within the endoplasmic reticulum; and (iv) substitution of Asp for Gly-91 completely blocked cell-cell fusion activity without affecting spike protein assembly or transport. These results argue that the conserved hydrophobic domain of SFV E1 is closely involved in membrane fusion and suggest that the homologous region in rotavirus VP4 may be involved in the entry pathway of this nonenveloped virus.
Treatment of Chronic Plaque Psoriasis by Selective Targeting of Memory Effector T Lymphocytes (2001)

Treatment with alefacept for 12 weeks is associated with improvement in chronic plaque psoriasis; some patients have a sustained clinical response after the cessation of treatment. Alefacept selectively targets CD45RO+ memory effector T lymphocytes, suggesting that they have a role in the pathogenesis of psoriasis.
Structure and Function of the Peripheral-Type Benzodiazepine Receptor in Steroidogenic Cells (1998)

Steroidogenesis depends on the rate of cholesterol transport from intracellular stores to the inner mitochondrial membrane cytochrome P-450 side-chain cleavage enzyme. Using steroidogenic cell submitochondrial fractions, mitochondrial preparations, various cell models, and animal models and with the help of pharmacological, biochemical, morphological, and molecular approaches, we provide evidence that the peripheral-type benzodiazepine receptor mediates the intramitochondrial cholesterol transport and the subsequent adrenal, gonadal, placental, and brain steroid biosynthesis.
Inserting Norplant capsules. (1991)

In a question-and-answer format Dr. Philip Darney describes the procedure for inserting NORPLANT a long-acting contraceptive implant. Darney an ob-gyn professor at the University of California San Francisco School of Medicine responds to questions from Dr. Ronald Chez an ob-gyn professor at University of South Florida College of Medicine. The insertion of NORPLANT is considered a minor office procedure. Darney explains that although NORPLANT is effective no matter where the capsules are placed removal is easier when the implants situated in the upper inner arm where there is less fat and easier surgical access. Women prefer to have the implants in the non- dominant arm. The procedure takes place under local anesthesia. After preparing the insertion site by cleansing it with an antiseptic solution a 2 mm incision is made. Usually only a sharp trocar is needed to make the incision. But if the skin is too tough or the trocar too dull a No. 11 scalpel is used. In order to facilitate removal the tips of the capsules are placed as close together as possible with the proximal ends being placed about 15 degrees apart thereby forming a fan-like pattern. This allows for the capsules to be removed through a single small incision. As Darney explains bleeding caused by the incision is minimal and its unlikely to result in an infection severe enough to require antibiotics or drainage. Furthermore a suture is never needed. Instead a compression dressing is used to protect the area from bruising and it is work for 24 hours.
Use of disease‐modifying medications for rheumatoid arthritis by race and ethnicity in the National Ambulatory Medical Care Survey (2011)

In the NAMCS, most visits coded with RA did not have an associated DMARD prescription. African Americans were less likely to receive DMARDs than whites, particularly when visiting nonrheumatologists.
NanoART Synthesis, Characterization, Uptake, Release and Toxicology for Human Monocyte–Macrophage Drug Delivery (2009)

These results support the continued development of macrophage-mediated nanoART carriage for HIV-1 disease.
The Innate Immune DNA Sensor cGAS Produces a Noncanonical Cyclic Dinucleotide that Activates Human STING (2013)

The presence of foreign DNA in the cytosol of mammalian cells elicits a potent antiviral interferon response. Recently, cytosolic DNA was proposed to induce the synthesis of cyclic GMP-AMP (cGAMP) upon binding to an enzyme called cGAMP synthase (cGAS). cGAMP activates an interferon response by binding to a downstream receptor called STING. Here, we identify natural variants of human STING (hSTING) that are poorly responsive to cGAMP yet, unexpectedly, are normally responsive to DNA and cGAS signaling. We explain this paradox by demonstrating that the cGAS product is actually a noncanonical cyclic dinucleotide, cyclic [G(2'-5')pA(3'-5')p], which contains a single 2'-5' phosphodiester bond. Cyclic [G(2'-5')pA(3'-5')p] potently activates diverse hSTING receptors and, therefore, may be a useful adjuvant or immunotherapeutic. Our results indicate that hSTING variants have evolved to distinguish conventional (3'-5') cyclic dinucleotides, known to be produced mainly by bacteria, from the noncanonical cyclic dinucleotide produced by mammalian cGAS.
The block-based trace cache (1999)

The trace cache is a recently proposed solution to achieving high instruction fetch bandwidth by buffering and reusing dynamic instruction traces. This work presents a new block-based trace cache implementation that can achieve higher IPC performance with more efficient storage of traces. Instead of explicitly storing instructions of a trace, pointers to blocks constituting a trace are stored in a much smaller trace table. The block-based trace cache renames fetch addresses at the basic block level and stores aligned blocks in a block cache. Traces are constructed by accessing the replicated block cache using block pointers from the trace table. Performance potential of the block-based trace cache is quantified and compared with perfect branch prediction and perfect fetch schemes. Comparing to the conventional trace cache, the block-based design can achieve higher IPC, with less impact on cycle time.Results: Using the SPECint95 benchmarks, a 16-wide realistic design of a block-based trace cache can improve performance 75% over a baseline design and to within 7% of a baseline design with perfect branch prediction. With idealized trace prediction, it is shown the block-based trace cache with an 1K-entry block cache achieves the same performance of the conventional trace cache with 32K entries.
Room temperature sputtering of inclined c-axis ZnO for shear mode solidly mounted resonators (2016)

ZnO films with a c-axis significantly inclined away from the surface normal were grown by a remote plasma sputtering technique at room temperature. The films were used to make solidly mounted resonators (SMRs) operating in shear mode at a resonant frequency of 1.35 GHz. Control of the ZnO microstructure was achieved using a polycrystalline AlN seed layer which can be added on top of a sputtered acoustic mirror to give a complete SMR device. The ZnO was reactively sputtered in an atmosphere of argon and oxygen from a zinc target. The c-axis of the ZnO was estimated to be at an angle of ∼45° to the surface normal. SMRs were measured to have quality factors (Q) of up to 140 and effective electromechanical coupling coefficients of up to 2.2% in air. Although an inclined c-axis can be achieved with direct growth onto the acoustic mirror, it is shown that the AlN seed layer provides higher coupling coefficients and narrower inclination angular distribution. The responses of the devices in liquids of different viscosities (acetone, water, and AZ5214E photoresist) were measured. The shear mode Q decreased by 45% in acetone, 72% in water, and 92% in AZ5214E.
Video deblocking with fine-grained scalable complexity for embedded mobile computing (2005)

This paper addresses the need of reducing blocking artifacts after video decompression in embedded mobile computing devices such as mobile phones and PDAs with limited computational capability, where low bit rate coding is usually employed and video deblocking is highly desirable. A novel video deblocking method has been developed which consists of two steps: deblocking mode decision and deblock filtering. Blocking artifacts are detected by examining the value of several adjacent pixels. Depending on the degree of blocking artifacts, a filter mode and a corresponding filtering center are determined for a region of pixels. The deblocking filter is chosen from five different types of candidates including variable center filters and nonsymmetric filters. Extensive experiments show that the proposed algorithm has achieved both lower computational complexity and better visual quality as compared to MPEG-4 VM. Furthermore, targeting the need of embedded mobile computing platforms, a scheme is developed to dynamically scale the complexity (and hence power consumption) of the deblocking algorithm with graceful visual quality degradation.
Processing of Highly Concentrated Aqueous α‐Alumina Suspensions Stabilized with Polyelectrolytes (1988)

Stability and rheology of aqueous α‐Al 2 O 3 suspensions with poly(methacrylic acid) and poly(acrylic acid) polyelectrolytes were studied as a function of pH, solids loading, and molecular weight. Past work has found polyelectrolyte‐stabilized suspensions to be fairly pH independent at low (e.g., 20 vol%) solids loadings. However, we now show that the effective pH range to provide dispersed and fluid suspensions narrows as the concentration of solids increases as related to interparticle forces. At high solids levels, the presence of excess polymer in solution has detrimental effects on stability, which increases as the molecular weight increases. Finally, with knowledge of these concepts, highly concentrated fluid suspensions of 60 vol% Al 2 O 3 (&gt;85 wt%) with submicrometer‐size particles have been processed. Higher consolidated densities and reduced sintering temperatures are attained when compared with more conventional processing techniques.
DC/DC Conversion Systems Consisting of Multiple Converter Modules: Stability, Control, and Experimental Verifications (2009)

This paper investigates DC/DC conversion systems constructed from connecting multiple converter modules in series and/or parallel at both the input and output sides. Control strategies aiming at achieving proper sharing of the voltage and/or current at the input or output sides are studied in detail. The relationship between sharing of input voltages/currents and that of output voltages/currents is studied. In particular, the inherent stability of control operations applied at the input side and the output side is analyzed. Based on the analysis, a general control strategy for series-parallel systems, which decouples the output voltage control loop and the sharing control loop, is proposed. Furthermore, three modularization architectures are proposed for input-series-output-parallel (ISOP), input-parallel-output-series (IPOS), and input-series-output-series (ISOS) connected systems. These architectures enjoy full advantages of modularization and no external controller is needed to coordinate the sharing control for the individual modules. Experimental prototypes are built and tested to validate the general control strategy and the proposed modularization architectures.
IEEE 802.22: the first worldwide wireless standard based on cognitive radios (2005)

In November/2004, we witnessed the formation of the first worldwide effort to define a novel wireless air interface standard based on cognitive radios (CRs): the IEEE 802.22 working group (WG). The IEEE 802.22 WG is chartered with the development of a CR-based wireless regional area network (WRAN) physical (PHY) and medium access control (MAC) layers for use by license-exempt devices in the spectrum that is currently allocated to the television (TV) service. Since 802.22 is required to reuse the fallow TV spectrum without causing any harmful interference to incumbents (i.e., the TV receivers), cognitive radio techniques are of primary importance in order to sense and measure the spectrum and detect the presence/absence of incumbent signals. On top of that, other advanced techniques that facilitate coexistence such as dynamic spectrum management and radio environment characterization could be designed. In this paper, we provide a detailed overview of the 802.22 architecture, its requirements, applications, and coexistence considerations that not only form the basis for the definition of this groundbreaking wireless air interface standard, but that will also serve as foundation for future research in the promising area of CRs
Transfer Learning from Speaker Verification to Multispeaker Text-To-Speech Synthesis (2018)

We describe a neural network-based system for text-to-speech (TTS) synthesis that is able to generate speech audio in the voice of many different speakers, including those unseen during training. Our system consists of three independently trained components: (1) a speaker encoder network, trained on a speaker verification task using an independent dataset of noisy speech from thousands of speakers without transcripts, to generate a fixed-dimensional embedding vector from seconds of reference speech from a target speaker; (2) a sequence-to-sequence synthesis network based on Tacotron 2, which generates a mel spectrogram from text, conditioned on the speaker embedding; (3) an auto-regressive WaveNet-based vocoder that converts the mel spectrogram into a sequence of time domain waveform samples. We demonstrate that the proposed model is able to transfer the knowledge of speaker variability learned by the discriminatively-trained speaker encoder to the new task, and is able to synthesize natural speech from speakers that were not seen during training. We quantify the importance of training the speaker encoder on a large and diverse speaker set in order to obtain the best generalization performance. Finally, we show that randomly sampled speaker embeddings can be used to synthesize speech in the voice of novel speakers dissimilar from those used in training, indicating that the model has learned a high quality speaker representation.