gebhart/patrepeval huggingface dataset:
A translational platform for prototyping closed-loop neuromodulation systems (2013)

While modulating neural activity through stimulation is an effective treatment for neurological diseases such as Parkinson's disease and essential tremor, an opportunity for improving neuromodulation therapy remains in automatically adjusting therapy to continuously optimize patient outcomes. Practical issues associated with achieving this include the paucity of human data related to disease states, poorly validated estimators of patient state, and unknown dynamic mappings of optimal stimulation parameters based on estimated states. To overcome these challenges, we present an investigational platform including: an implanted sensing and stimulation device to collect data and run automated closed-loop algorithms; an external tool to prototype classifier and control-policy algorithms; and real-time telemetry to update the implanted device firmware and monitor its state. The prototyping system was demonstrated in a chronic large animal model studying hippocampal dynamics. We used the platform to find biomarkers of the observed states and transfer functions of different stimulation amplitudes. Data showed that moderate levels of stimulation suppress hippocampal beta activity, while high levels of stimulation produce seizure-like after-discharge activity. The biomarker and transfer function observations were mapped into classifier and control-policy algorithms, which were downloaded to the implanted device to continuously titrate stimulation amplitude for the desired network effect. The platform is designed to be a flexible prototyping tool and could be used to develop improved mechanistic models and automated closed-loop systems for a variety of neurological disorders.
Conditional Degrons for Controlling Protein Expression at the Protein Level (2017)

The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
Serial Analysis of Gene Expression in the Chicken Otocyst (2011)

The inner ear arises from multipotent placodal precursors that are gradually committed to the otic fate and further differentiate into all inner ear cell types, with the exception of a few immigrating neural crest-derived cells. The otocyst plays a pivotal role during inner ear development: otic progenitor cells sub-compartmentalize into non-sensory and prosensory domains, giving rise to individual vestibular and auditory organs and their associated ganglia. The genes and pathways underlying this progressive subdivision and differentiation process are not entirely known. The goal of this study was to identify a comprehensive set of genes expressed in the chicken otocyst using the serial analysis of gene expression (SAGE) method. Our analysis revealed several hundred transcriptional regulators, potential signaling proteins, and receptors. We identified a substantial collection of genes that were previously known in the context of inner ear development, but we also found many new candidate genes, such as SOX4, SOX5, SOX7, SOX8, SOX11, and SOX18, which previously were not known to be expressed in the developing inner ear. Despite its limitation of not being all-inclusive, the generated otocyst SAGE library is a practical bioinformatics tool to study otocyst gene expression and to identify candidate genes for developmental studies.
Spinal cord stimulation reduces hypersensitivity through activation of opioid receptors in a frequency‐dependent manner (2012)

These results suggest that both 4- and 60-Hz SCS, in part, work through opioid receptor mechanisms, with 4-Hz SCS activating μ-opioid receptors while 60-Hz SCS activated δ-opioid receptors.
Transdermal optical renal function monitoring in humans: development, verification, and validation of a prototype device (2018)

A prototype medical device for monitoring kidney function by transdermal measurement of the clearance rate of the exogenous fluorescent tracer agent MB-102 (administered intravenously) was developed. Verification of the device with an in vitro protocol is described. The expected renal clearance of the agent was mimicked by preparing a dilution series of MB-102 in the presence of a scattering agent. The slope of a linear fit to the logarithm of fluorescence intensity as a function of dilution step agreed with predictions within 5%, a level of accuracy that would be adequate in assessment of GFR to prevent misdiagnosis of kidney disease. Transdermal measurement was validated using a rat model. A two-compartment pharmacokinetic dependence was observed, with equilibration of the fluorescent agent between the vascular space into which it was injected and the extracellular space into which it subsequently diffused. The best observed signal-to-noise ratios were about 150, allowing determination of the renal clearance time with 5% precision using a 10-min fitting window. Based on the verification and validation methods for transdermal fluorescence detection described herein, the instrument has been approved by the FDA for a first-in-human clinical study, and a first transdermal clearance curve in a human is presented herein.
Transient Diabetes Insipidus After Discontinuation of Therapeutic Vasopressin (2004)

The use of vasopressin for the treatment of septic shock is increasing. Few reports of fluid and electrolyte complications of this therapy have been reported. A neurologically impaired, 53-year-old man with a history of syndrome of inappropriate antidiuretic hormone developed apparent transient diabetes insipidus and acute hypernatremia after being treated with vasopressin. He was treated for presumed septic shock with intravenous vasopressin 0.01-0.10 U/minute. His blood pressure did not improve with this therapy, and his course was complicated by hyponatremia during the vasopressin infusion. Discontinuation of the infusion was followed by a profound (8.4 L) diuresis and rapid onset of hypernatremia (serum sodium concentration increased from 132 to 157 mEq/L over 8 hrs). Although urine osmolality was not measured during the patient's diuresis, the rapid changes in serum sodium concentration can be explained only by an inappropriate water diuresis. The diuresis ceased when the vasopressin infusion was resumed. We concluded that these findings are most consistent with transient diabetes insipidus. The safety and efficacy of intravenous vasopressin have not been established in patients with septic shock and underlying disorders of water homeostasis. The drug may have diminished vasoconstrictive effects in this patient population. Careful monitoring of water and sodium balance is warranted in all patients treated with vasopressin for septic shock.
Recent developments in the discovery of protein kinase inhibitors from the urea class. (2004)

With two compounds on the market (Gleevec and Iressa), and a number of drug candidates in late-stage clinical trials, small-molecule kinase inhibitors hold great potential as novel therapies for cancer and inflammatory disorders. Inhibitors from the urea class were first reported in 1996 and have emerged as an important compound class for medicinal chemists due to their unique binding mode and kinase inhibition profile. Currently, five members of this class are undergoing clinical trials, BIRB-796 (Boehringer Ingelheim Pharmaceuticals Inc), BAY-43-9006 (Bayer AG/Onyx Pharmaceuticals Inc), CP-547632 (Pfizer Inc), MLN-518 (Millennium Pharmaceuticals Inc) and KRN-951 (Kirin Brewery Co Ltd). This review focuses on the most recent developments in the discovery of urea-based protein kinase inhibitors.
Nude mouse metastatic models of human stomach cancer constructed using orthotopic implantation of histologically intact tissue. (1993)

Nude mice have been used to develop s.c. growing human stomach tumors, but these rarely metastasize. Recently, I. J. Fidler and others have developed orthotopic implantation metastatic models using cell suspensions which are inoculated into the corresponding organ of nude mice from which the tumor cells were originally derived in the human. However, recent work has indicated that disaggregated cell suspensions may not always express their full metastatic potential. In this light, we have recently developed an orthotopic implant model utilizing intact tissue such as that obtained directly from surgery. This approach has yielded high take rates and frequent metastases in colon cancer, bladder cancer, lung cancer, pancreatic cancer, and prostate cancer. We report here the application of this intact tissue orthotopic implant technique to stomach cancer resulting in the formation of metastases in 100% of the mice with extensive primary growth to the regional lymph nodes, liver, and lung. In contrast, when cell suspensions were used to inject stomach cancer cells at the same site, metastases occurred in only 6.7% of the mice with local tumor formation, emphasizing the importance of using intact tissue to allow full expression of metastatic potential. Injuring the serosa similar to that occurring in intact tissue transplantation did not increase the metastatic rate after orthotopic injection of cell suspensions of stomach tumor cells. This intact tissue orthotopic implantation model should allow development of new treatment modalities and further study of the biology of human stomach cancer.
The Programmed Death-1 Immune-Suppressive Pathway: Barrier to Antitumor Immunity (2014)

Programmed death ligand 1 (PD-L1, also known as B7 homolog 1 or CD274) is a major obstacle to antitumor immunity because it tolerizes/anergizes tumor-reactive T cells by binding to its receptor programmed death-1 (CD279), renders tumor cells resistant to CD8(+) T cell- and FasL-mediated lysis, and tolerizes T cells by reverse signaling through T cell-expressed CD80. PD-L1 is abundant in the tumor microenvironment, where it is expressed by many malignant cells, as well as by immune cells and vascular endothelial cells. The critical role of PD-L1 in obstructing antitumor immunity has been demonstrated in multiple animal models and in recent clinical trials. This article reviews the mechanisms by which PD-L1 impairs antitumor immunity and discusses established and experimental strategies for maintaining T cell activation in the presence of PD-L1-expressing cells in the tumor microenvironment.
Waist circumference, abdominal obesity, and depression among overweight and obese U.S. adults: national health and nutrition examination survey 2005-2006 (2011)

Among overweight and obese U.S. adults, waist circumference or abdominal obesity was significantly associated with increased likelihoods of having major depressive symptoms or moderate-to-severe depressive symptoms. Thus, mental health status should be monitored and evaluated in adults with abdominal obesity, particularly in those who are overweight.
Transforming growth factors produced by certain human tumor cells: polypeptides that interact with epidermal growth factor receptors. (1980)

Three different human tumor lines in culture, a rhabdomyosarcoma, a bronchogenic carcinoma and a metastatic melanoma, release proteins (transforming growth factors, TGFs) into the medium that confer the transformed phenotype on untransformed fibroblasts. These proteins are acid and heat-stable; produce profound morphologic changes in rat and human fibroblasts; and enable normal anchorage-dependent cells to grow in agar. Removal of the transforming protein results in a reversion of cell phenotype. The major activity interacts with epidermal growth factor (EGF) cell membrane receptors. The peptides from these tumor cells are similar in their action to the sarcoma growth factor (SGF) released by murine sarcoma virus-transformed rodent cells. The most anchorage-independent tumor cells released the most TGFs. EGF-related TGFs were not detectable in fluids from cultures of cells with high numbers of free EGF membrane receptors (normal human fibroblasts and human carcinomas).
Effect of the Antiarrhythmic Agent Moricizine on Survival after Myocardial Infarction (1992)

As with the antiarrhythmic agents used in CAST-I (flecainide and encainide), the use of moricizine in CAST-II to suppress asymptomatic or mildly symptomatic ventricular premature depolarizations to try to reduce mortality after myocardial infarction is not only ineffective but also harmful.
Measurement and manipulation of van der Waals forces in atomic-force microscopy (1994)

An understanding of the interaction between tip and sample in atomic-force microscopy is needed to interpret atomic-force-microscope (AFM) images. In contact mode, the strength of the van der Waals (vdW) force sets image resolution; in noncontact mode, local gradients in the vdW force are imaged. By immersing tip and sample in an appropriate fluid, we can decrease the vdW forces and even change their sign. Selecting a fluid that leads to a small repulsive vdW force can greatly improve image resolution and eliminates problems caused by the well-known tip-snapping instability. To measure the vdW interactions produced by different fluids, we have developed ways to calibrate the spring constant and sharpness of AFM tips and to measure accurately the Hamaker constant of vdW interactions. These techniques show that the AFM can be used for local force measurements with an accuracy approaching that of surface-force apparatuses. As an example, we have observed the crossover from nonretarded to retarded vdW forces between a silicon nitride tip and a mica sample in air.
Depth filtering of first breaks and ground roll (1991)

Abstract Much of the energy removed in a typical standard seismic data preprocessing sequence corresponds to approximately horizontal propagation in very near-surface structure. Such energy includes direct (first-break) compressional waves, direct shear waves, and ground roll; these may be effectively separated from deeper reflections by downward continuation of the recorded common-source wavefield, by reverse-time extrapolation, to a depth beneath which these waves propagate. The subhorizontally traveling waves get left behind in the shallow part of the model. Subsequent upward continuation of the wavefield reconstructs the original surface-recorded wavefield with the subhorizontally traveling waves removed. Only a very simple (even constant) velocity distribution is required for the wavefield extrapolation; no net distortion is produced since both downward and upward continuations are performed using the same velocity model.
Understanding and Capturing People’s Privacy Policies in a People Finder Application (2018)

A number of mobile applications have emerged that allow users to locate one another. However, people have expressed concerns about the privacy implications associated with this class of software, suggesting that broad adoption may only happen to the extent that these concerns are adequately addressed. In this article, we report on our work on PEOPLEFINDER, an application that enables cell phone and laptop users to selectively share their locations with others (e.g. friends, family, and colleagues). The objective of our work has been to better understand people’s attitudes and behaviors towards privacy as they interact with such an application, and to explore technologies that empower users to more effectively and efficiently specify their privacy preferences (or “policies”). These technologies include user interfaces for specifying rules and auditing disclosures, as well as machine learning techniques to see if the system can help people manage their policies better. We present evaluations of these technologies in the context of one laboratory study and three field studies.
Large‐scale analysis of the barley transcriptome based on expressed sequence tags (2004)

To provide resources for barley genomics, 110,981 expressed sequence tags (ESTs) were generated from 22 cDNA libraries representing tissues at various developmental stages. This EST collection corresponds to approximately one-third of the 380,000 publicly available barley ESTs. Clustering and assembly resulted in 14,151 tentative consensi (TCs) and 11 073 singletons, altogether representing 25 224 putatively unique sequences. Of these, 17.5% showed no significant similarity to other barley ESTs present in dbEST. More than 41% of all barley genes are supposed to belong to multigene families and approximately 4% of the barley genes undergo alternative splicing. Based on the functional annotation of the set of unique sequences, the functional category 'Energy' was further analysed to reveal tissue- and stage-specific differences in gene expression. Hierarchical clustering of 362 differentially expressed TCs resulted in the identification of seven major clusters. The clusters reflect biochemical pathways predominantly activated in specific tissues and at various developmental stages. During seed germination glycolysis could be identified as the most predominant biochemical pathway. Germination-specific glycolysis is characterized by the coordinated expression of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase, whose antagonistic actions possibly regulate the flux of amino acids into protein biosynthesis and gluconeogenesis respectively. The expression of defence-related and antioxidant genes during germination might be controlled by the ethylene-signalling pathway as concluded from the coordinated expression of those genes and the transcription factors (TF) EIN3 and EREBPG. Moreover, because of their predominant expression in germinating seeds, TF of the AP2 and MYB type are presumably major regulators of germination.
Folding-Unfolding Transitions in Single Titin Molecules Characterized with Laser Tweezers (1997)

Titin, a giant filamentous polypeptide, is believed to play a fundamental role in maintaining sarcomeric structural integrity and developing what is known as passive force in muscle. Measurements of the force required to stretch a single molecule revealed that titin behaves as a highly nonlinear entropic spring. The molecule unfolds in a high-force transition beginning at 20 to 30 piconewtons and refolds in a low-force transition at approximately 2.5 piconewtons. A fraction of the molecule (5 to 40 percent) remains permanently unfolded, behaving as a wormlike chain with a persistence length (a measure of the chain's bending rigidity) of 20 angstroms. Force hysteresis arises from a difference between the unfolding and refolding kinetics of the molecule relative to the stretch and release rates in the experiments, respectively. Scaling the molecular data up to sarcomeric dimensions reproduced many features of the passive force versus extension curve of muscle fibers.
Use of N‐acetylethyleneimine [AEI] for the inactivation of semliki forest virus in vitro (1986)

N-Acetylethyleneimine (AEI) was used to inactivate the avirulent Togavirus Semliki Forest virus (A774 strain) grown in chick embryo, Vero, and brain cell cultures. The purity of the virus preparation affected the kinetics of inactivation. The rate of inactivation increased with a rise in temperature from 5 to 40 degrees C and in concentration of AEI from 0.025 to 0.1%. The resultant vaccine was inoculated into adult mice to test its antigenicity and into suckling mice to test for the presence of infective virus. Semliki Forest virus-specific IgG was produced equal to that of mice given live virus, and mice were protected against the lethal SFV L10 strain. No suckling mice died, and the brains of the adult mice showed no pathology.
Comparison of the Efficacy and Safety of Latanoprost 0.005% Compared to Brimonidine 0.2% or Dorzolamide 2% When Added to a Topical β-Adrenergic Blocker in Patients with Primary Open-Angle Glaucoma or Ocular Hypertension (2000)

The purpose of this study was to evaluate the ocular hypotensive efficacy and safety of latanoprost 0.005% (Xalatan, Pharmacia & Upjohn), brimonidine (Alphagan, Allergan), and dorzolamide (Trusopt, Merck Inc.) when added to a beta-blocker in patients with ocular hypertension or primary open-angle glaucoma. This was a multicenter, retrospective analysis which included all reviewed patient records in which latanoprost, brimonidine or dorzolamide were added to a beta-blocker for at least three months. Patients who were treated for less than three months, who failed therapy due to ineffectiveness of the medicine or an adverse event also were included. The study included 141 patients. Latanoprost (n = 50) showed an intraocular pressure of 16.7 +/- 3.3 mm Hg (-6.3 +/- 4.1 mm Hg, P < 0.001), brimonidine (n = 24) 17.4 +/- 4.9 mm Hg (-4.2 +/- 4.5 mm Hg, P < 0.001), and dorzolamide (n = 67) 20.1 +/- 6.1 mm Hg (-3.1 +/- 5.1 mm Hg, P < 0.001) at three months. A significant difference was observed in the absolute level of intraocular pressure (P < 0.005) and the change from baseline between groups (P < 0.005) at three months. A significant difference was observed between groups in the success rate of therapy between latanoprost (70%), brimonidine (58%) and dorzolamide (40%) (P = 0.008). No significant differences were observed between groups for rate or type of adverse events leading to discontinued therapy. This study showed that latanoprost, when added to beta-blockers, compares favorably in ocular hypotensive efficacy and is similar in safety to brimonidine and dorzolamide.
Rabies ribonucleocapsid as an oral immunogen and immunological enhancer. (1994)

The administration of rabies ribonucleocapsid (RNP) by oral as well as parenteral routes was found to prime specific T cells and elicit N-protein-specific antibodies. per os and intramuscular immunization led to the production of antibodies of the IgA and IgG isotypes, respectively. Mice primed orally with RNP produced significantly enhanced amounts of virus-neutralizing antibody, compared with non-immune controls, upon subsequent parenteral booster immunization with inactivated rabies virus. Thus oral immunization with rabies RNP primed cells capable of mediating a secondary systemic response to rabies virus. The results of experiments in which peptide and protein antigens were administered either physically coupled to or mixed with RNP indicate that RNP has an inherent capacity to enhance immune responses.