gebhart/patrepeval huggingface dataset:
On the Control of the Berkeley Lower Extremity Exoskeleton (BLEEX) (2006)

The first functional load-carrying and energetically autonomous exoskeleton was demonstrated at U.C. Berkeley, walking at the average speed of 1.3 m/s while carrying a 34 kg (75 lb) payload. Four fundamental technologies associated with the Berkeley Lower Extremity Exoskeleton (BLEEX) were tackled during the course of this project. These four core technologies include: the design of the exoskeleton architecture, control schemes, a body local area network (bLAN) to host the control algorithm and an on-board power unit to power the actuators, sensors and the computers. This article gives an overview of one of the control schemes. The analysis here is an extension of the classical definition of the sensitivity function of a system: the ability of a system to reject disturbances or the measure of system robustness. The control algorithm developed here increases the closed loop system sensitivity to its wearer’s forces and torques without any measurement from the wearer (such as force, position, or electromyogram signal). The control method has little robustness to parameter variations and therefore requires a relatively good dynamic model of the system. The tradeoffs between having sensors to measure human variables and the lack of robustness to parameter variation are described.
HIV-1-infected monocyte-derived dendritic cells do not undergo maturation but can elicit IL-10 production and T cell regulation (2004)

Dendritic cells (DCs) undergo maturation during virus infection and thereby become potent stimulators of cell-mediated immunity. HIV-1 replicates in immature DCs, but we now find that infection is not accompanied by many components of maturation in either infected cells or uninfected bystanders. The infected cultures do not develop potent stimulating activity for the mixed leukocyte reaction (MLR), and the DCs producing HIV-1 gag p24 do not express CD83 and DC-lysosome-associated membrane protein maturation markers. If different maturation stimuli are applied to DCs infected with HIV-1, the infected cells selectively fail to mature. When DCs from HIV-1-infected patients are infected and cultured with autologous T cells, IL-10 was produced in 6 of 10 patients. These DC-T cell cocultures could suppress another immune response, the MLR. The regulation was partially IL-10-dependent and correlated in extent with the level of IL-10 produced. Suppressor cells only developed from infected patients, rather than healthy controls, and the DCs had to be exposed to live virus rather than HIV-1 gag peptides or protein. These results indicate that HIV-1-infected DCs have two previously unrecognized means to evade immune responses: maturation can be blocked reducing the efficacy of antigen presentation from infected cells, and T cell-dependent suppression can be induced.
New assay to detect low‐affinity interactions and characterization of leukocyte receptors for collagen including leukocyte‐associated Ig‐like receptor‐1 (LAIR‐1) (2009)

Leukocyte activity is controlled by numerous interactions between membrane receptors and ligands on the cell surface. These interactions are of low affinity making detection difficult. We developed a sensitive assay that could readily detect extremely weak interactions such as that between CD200 and the activating receptor CD200RLa (K(d)>500 microM) at the protein level. We used the new technology to screen for interactions of inhibitory receptors for collagens. We confirmed that both human and mouse leukocyte-associated Ig-like receptor-1, and in addition the related inhibitory leukocyte Ig-like receptor subfamily B member 4 (CD85K, Gp49B), bound collagen specifically, whereas other cell surface proteins gave no binding. The monomeric affinities of the interactions were then determined to allow comparison with other leukocyte interactions and indicate conditions when these interactions might lead to inhibitory signals.
Diabetes mellitus and free radicals (1993)

Diabetes mellitus is a syndrome initially characterized by a loss of glucose homeostasis. The disease is progressive and is associated with high risk of atherosclerosis, kidney and nerve damage as well as blindness. Abnormalities in the regulation of peroxide and transition metal metabolism are postulated to result in establishment of the disease as well as its longer term complications. Diabetes mellitus is associated with oxidative reactions, particularly those which are catalyzed by decompartmentalized transition metals, but their causative significance in diabetic tissue damage remains to be established.
A New Procedure Allowing the Complete Removal and Prevention of Hemodialysis Biofilms (2005)

Most currently used disinfectants for dialysis machines have a good bactericidal efficacy on biofilms but leave dead cells on the surface. This contributes to the regrowth of biofilm and the release of pyrogens. A new anti-biofilm procedure consisting of sequential treatment combining enzymes and detergents is able to detach adherent cells. The efficacy of this procedure was assessed both in vitro and in reality. For in vitro studies, a biofilm model was set up. Studies were also performed in reality in a clinically used dialysis machine. Biofilm removal was first monitored by image analysis. Then, the biomass was detached by scraping and quantified by plate counts and endotoxin level measurement. Treated samples were compared to untreated control samples. The procedure led to the complete detachment of the biomass, both in vitro and in the reality situation. The aim of this procedure is to replace or complete the usual disinfection methods for medical devices.
Angiomotin and angiomotin like proteins, their expression and correlation with angiogenesis and clinical outcome in human breast cancer (2006)

Angiomotin, a putative endothelial motility factor, is highly expressed in human breast tumour tissues and linked to angiogenesis. It links to the aggressive nature of breast tumours and the long term survival of the patients. These data point angiomotin as being a potential therapeutic target.
Group II Introns: Mobile Ribozymes that Invade DNA (2010)

Group II introns are mobile ribozymes that self-splice from precursor RNAs to yield excised intron lariat RNAs, which then invade new genomic DNA sites by reverse splicing. The introns encode a reverse transcriptase that stabilizes the catalytically active RNA structure for forward and reverse splicing, and afterwards converts the integrated intron RNA back into DNA. The characteristics of group II introns suggest that they or their close relatives were evolutionary ancestors of spliceosomal introns, the spliceosome, and retrotransposons in eukaryotes. Further, their ribozyme-based DNA integration mechanism enabled the development of group II introns into gene targeting vectors ("targetrons"), which have the unique feature of readily programmable DNA target specificity.
Malonylierungsreaktionen an 4‐monosubstituierten Pyrazolidin‐3,5‐dionen (1975)

Abstract Reaktionen 4‐monosubstituierter Pyrazolidin‐3,5‐dione 1A , B mit Malonylchloriden 2 führen zu 1 H ,5 H ‐Pyrazolo[1,2‐ a ]pyrazolen 3A , B . In Gegenwart von Pyridin (Triäthylamin) fallen die genannten Verbindungen als Salze 4 an. Die Behandlung von 4Ah , i mit wäßriger Salzsäure verläuft unter Spaltung der (CN)‐Bindung zu den Pyrazolidin‐3,5‐dionen 5Ah , i . Die Alkoholyse von 3Bh , i führt in analoger Weise zu 7Bh , i . Während die Cyclisierung von 1A , B mit 2g ohne Basenzusatz zu den Chloraddukten 8A , B führt, kann bei Anwesenheit äquimolarer Mengen Base 9 Ag isoliert werden. Die Synthesemöglichkeit von 9A , B ist weitgehend abhängig von der Natur des Lösungsmittels, der angewandten Temperatur, der Reaktionsdauer und vom Substitutionsmuster der Malonylchloride 2 . Unter Baseneinfluß lagern sich die Oxazine 9A , B irreversibel in die entsprechenden Salze 4A , B um.
A novel SiGe-inserted SOI structure for high performance PDSOI CMOSFETs (2002)

A novel partially-depleted silicon-on-insulator (PDSOI) CMOSFETs with SiGe-inserted layer have been proposed. The SiGe-inserted layer in NMOS successively suppresses the floating body effects (FBE) by lowering the body-to-source potential barrier to hole current. It also provides a good current performance in PMOS by inducing the change of channel dopant distribution and increasing the efficiency of pocket ion implantation. Consequently, SiGe-inserted SOI devices achieve higher drain-to-source breakdown voltage in NMOS due to the suppression of FBE and increase drive currents of both NMOS and PMOS by 10% and 15%, respectively, compared to conventional PDSOI devices.
A Microfluidic Oxygenator for Biological Cell Culture (2007)

In this paper, we report on the development of a microfluidic platform in which dissolved oxygen (DO) concentrations can be dynamically adjusted for cell culture applications. The DO concentration in culture media flowing through enclosed microchannels is regulated by the diffusion through an elastromeric interface from an overhead gas channel, using an oxygen-sensitive dye embedded in the fluid channel as a sensor. Using a microchannel network functioning as an oxygen/nitrogen mixer, the growth characteristics of murine fibroblast cells (3T3) were analyzed as a function of eight discrete DO concentrations in culture media within a single device, ranging from anaerobic (0 ppm) to fully saturated (42 ppm).
The myocardin family of transcriptional coactivators: versatile regulators of cell growth, migration, and myogenesis (2006)

The association of transcriptional coactivators with sequence-specific DNA-binding proteins provides versatility and specificity to gene regulation and expands the regulatory potential of individual cis-regulatory DNA sequences. Members of the myocardin family of coactivators activate genes involved in cell proliferation, migration, and myogenesis by associating with serum response factor (SRF). The partnership of myocardin family members and SRF also controls genes encoding components of the actin cytoskeleton and confers responsiveness to extracellular growth signals and intracellular changes in the cytoskeleton, thereby creating a transcriptional-cytoskeletal regulatory circuit. These functions are reflected in defects in smooth muscle differentiation and function in mice with mutations in myocardin family members. This article reviews the functions and mechanisms of action of the myocardin family of coactivators and the physiological significance of transcriptional coactivation in the context of signal-dependent and cell-type-specific gene regulation.
Neuroactive Steroids. 1. Positive Allosteric Modulators of the (γ-Aminobutyric Acid) A Receptor: Structure–Activity Relationships of Heterocyclic Substitution at C-21 (2015)

Neuroactive steroids (NASs) have been shown to impact central nervous system (CNS) function through positive allosteric modulation of the GABA(A) receptor (GABA(A)-R). Herein we report the effects on the activity and pharmacokinetic properties of a series of nor-19 pregnanolone analogues bearing a heterocyclic substituent at C-21. These efforts resulted in the identification of SGE-516, a balanced synaptic/extrasynaptic GABA(A) receptor modulator, and SGE-872, a selective extrasynaptic GABA(A) receptor modulator. Both molecules possess excellent druglike properties, making them advanced leads for oral delivery of GABA(A) receptor modulators.
Growth hormones. 1. Polymorphism. (Minireview) (1988)

Pituitary growth hormone (GH) is not a single molecular species, but a whole set of similar molecules, the individual specific characteristics of which constitute the polymorphism of this hormone. The present paper deals mainly with various forms of human GH, called "variants", and touches on this polymorphism in other species as well. The 22 K variant (MW = 22,000 daltons) is the predominant form of GH to which all other variants are compared as to chemical structure and biological effect. These variants are classified into two large groups: 1) mass variants, the molecular weight of which is modified in comparison with that of 22 K; these can be subdivided into aggregated and non-aggregated forms, and 2) charge variants with modified electrophoretic mobility. Outside this classification are entities which are not yet well known; these include bioinactive GH, correctly detected by RIA but deprived of biological activity or, on the contrary, strongly bioactive GH lacking immunoreactivity and consequently difficult to study. Another outsider is the SV-hGH-2 variant encoded from a gene different from the hGH-N gene normally coding for the other variants. In this case, the product could be considered a true isohormone of 22 K and no longer a variant. The pituitary expression of this gene has never been evidenced to date, but according to recent data, it could be expressed at the placental level and be implicated in human placental growth hormone (hPGH) synthesis. hPGH is a newly-found GH in pregnant women which takes over pituitary GH from the 25th week onwards. After the GH molecules are released by the pituitary in the blood stream, they are partially taken up and carried by binding proteins. The physiological role of this phenomenon could be the setting up of a GH reservoir and a GH sparing process since the metabolic clearance rate of the complex GH-binding protein is slower than that of free GH, thus increasing the biological half-life of the hormone.
Cardiac hypertrophy is associated with altered thioredoxin and ASK-1 signaling in a mouse model of menopause (2008)

Oxidative stress is implicated in menopause-associated hypertension and cardiovascular disease. The role of antioxidants in this process is unclear. We questioned whether the downregulation of thioredoxin (TRX) is associated with oxidative stress and the development of hypertension and target-organ damage (cardiac hypertrophy) in a menopause model. TRX is an endogenous antioxidant that also interacts with signaling molecules, such as apoptosis signal-regulated kinase 1 (ASK-1), independently of its antioxidant function. Aged female wild-type (WT) and follitropin receptor knockout (FORKO) mice (20-24 wk), with hormonal imbalances, were studied. Mice were infused with ANG II (400 ng x kg(-1) x min(-1); 14 days). Systolic blood pressure was increased by ANG II in WT (166+/-8 vs. 121+/-5 mmHg) and FORKO (176+/-7 vs. 115+/-5 mmHg; P<0.0001; n=9/group) mice. In ANG II-infused FORKO mice, cardiac mass was increased by 42% (P<0.001). This was associated with increased collagen content and augmented ERK1/2 phosphorylation (2-fold). Cardiac TRX expression and activity were decreased by ANG II in FORKO but not in WT (P<0.01) mice. ASK-1 expression, cleaved caspase III content, and Bax/Bcl-2 content were increased in ANG II-infused FORKO (P<0.05). ANG II had no effect on cardiac NAD(P)H oxidase activity or on O(2)(*-) levels in WT or FORKO. Cardiac ANG II type 1 receptor expression was similar in FORKO and WT. These findings indicate that in female FORKO, ANG II-induced cardiac hypertrophy and fibrosis are associated with the TRX downregulation and upregulation of ASK-1/caspase signaling. Our data suggest that in a model of menopause, protective actions of TRX may be blunted, which could contribute to cardiac remodeling independently of oxidative stress and hypertension.
Opportunities and obstacles for deep learning in biology and medicine (2018)

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
Relationships among Resonant Frequency Changes on a Coated Quartz Crystal Microbalance, Thickness Changes, and Resistance Responses of Polymer−Carbon Black Composite Chemiresistors (2000)

The relationships among frequency changes on a film-coated quartz crystal microbalance, thickness changes, and dc resistance changes have been investigated for carbon black-insulating polymer composite vapor detectors. Quartz crystal microbalance (QCM) measurements and ellipsometry measurements have been performed simultaneously on polymer films that do not contain carbon black filler to relate the QCM frequency change and the ellipsometrically determined thickness change to the analyte concentration in the vapor phase. In addition, quartz crystal microbalance measurements and dc resistance measurements on carbon black composites of these same polymers have been performed simultaneously to relate the QCM frequency change and dc electrical resistance response to the analyte concentration in the vapor phase. The data indicate that the dc resistance change is directly relatable to the thickness change of the polymers and that a variety of analytes that produce a given thickness change produce a constant resistance change for each member of the test set of polymers investigated in this work.
Precipitation of Mixtures of Anionic Surfactants (1992)

The tendency of an anionic surfactant to precipitate can be quantified in two different ways: (1) as a Krafft temperature or temperature below which surfactant precipitate appears, or (2) as a hardness or salinity tolerance - the minimum concentration of cation precipitating with the surfactant anion which is required to form any precipitate. Surfactants used in practical applications can contain many surfactant components, but these components are often similar enough so that they form nearly ideal mixed micelles. Yet precipitate initially formed from these mixtures contains only the one component most easily precipitated. As a result, the tendency of a multicomponent surfactant mixture to precipitate can be substantially less than that of a pure component typical of the mixture present at the same concentration.
Underdiagnosis of Peripheral Neuropathy in Type 2 Diabetes (2005)

Diabetic peripheral neuropathy and its late sequelae cost >$4 billion annually in the U.S. (1). Improved glycemic control, early detection, and preventive care can prevent or delay adverse outcomes (2–4). An annual foot exam, which may include monofilament testing, is recommended by the American Diabetes Association (5). Unfortunately, neuropathy screening is underutilized in primary care practice (6,7). The GOAL A1C (Glycemic Optimization with Algorithms and Labs At Po1nt of Care) study assessed methods of A1C testing and insulin titration monitoring strategies in a large nationwide sample of predominantly primary care patients with type 2 diabetes. At baseline, physician perception of the presence of neuropathy was assessed via a survey before monofilament testing. A comparison between physician perception and monofilament testing is reported.

GOAL A1C was a randomized, open-label, parallel, four-arm study that compared the impact of point of care versus laboratory A1C testing and weekly versus less frequent insulin titration monitoring on glycemic control in patients with type 2 diabetes adding insulin glargine to existing oral antidiabetic therapy. Eligible patients were aged ≥18 years, inadequately controlled on oral antidiabetic agents (A1C >7.0%), and candidates for insulin. All signed informed consent …
Athermal silica-based arrayed-waveguide grating (AWG) multiplexers with new low loss groove design (2003)

We propose a new low loss groove design for athermal silica-based arrayed-waveguide grating multiplexers. The insertion loss was 3 dB and the cross talk was -35 dB. The temperature dependence of the channel wavelength change was suppressed to below 0.4 nm in the 0-85/spl deg/C temperature range.
Oligonucleotide-directed mutagenesis by microscale ‘shot-gun’ gene synthesis (1985)

We describe a rapid and efficient microscale method for in vitro site-directed mutagenesis by gene synthesis. Mutants are constructed by "shot-gun ligation" of overlapping synthetic oligonucleotides yielding double stranded synthetic DNA of more than 120 nucleotides in length. The terminal oligonucleotides of the DNA segment to be synthesized are designed to create sticky ends complementary to unique restriction sites of a polylinker present in an M13 vector. The oligonucleotides are hybridized and ligated to the M13 vector without any purification of the synthetic DNA segment. After cloning, about half of the progeny from such shot-gun ligations contained the predicted sequence demonstrating the efficacy of this method for gene synthesis and its potential for the extensive mutational analysis of genes.
Current strategies in previously untreated advanced colorectal cancer. (2004)

Colorectal cancer is the second most common cause of cancer-related death in the United States. Approximately 30% to 40% of patients with colorectal cancer have locoregionally advanced or metastatic disease on presentation and cannot be cured with surgical therapy. After many years without significant change, systemic therapy for colorectal cancer is rapidly evolving. The past decade has seen the introduction of new chemotherapeutic agents such as irinotecan (Camptosar), oxaliplatin (Eloxatin) and the oral 5-FU prodrug capecitabine (Xeloda). Combination studies of these new agents with the standard 5-FU/leucovorin have extended median survival in patients with advanced colorectal cancer for up to 21 months. In addition, targeted agents with activity in colorectal cancer have emerged and are promising. This article reviews the current treatment recommendations for patients who present with advanced colorectal cancer. Survival in patients with advanced colorectal cancer is on a positive trajectory. The hope that some patients with advanced disease will be long-term survivors (even without surgery) appears to be within the range of possibility.
Long-term randomized controlled trial of a novel nanopowder hemostatic agent (TC-325) for control of severe arterial upper gastrointestinal bleeding in a porcine model (2011)

TC-325 is safe and highly effective in achieving hemostasis in an anticoagulated severe arterial gastrointestinal bleeding animal model.