gebhart/patrepeval huggingface dataset:
Phosphorylation of Adenohypophyseal Plasma Membranes and Properties of Associated Protein Kinase (1974)

Abstract Plasma membranes isolated from bovine anterior pituitary gland are self-phosphorylated in the presence of [γ-32P]ATP by an endogenous protein kinase. Eighty per cent of protein kinase activity is solubilized by treatment of the plasma membranes with 1.0 n NH4Cl or 0.5% Triton X-100. The presence of latent protein kinase activity is shown by an approximately 50% increase of total enzymatic activity upon addition of the detergent. The enzyme associated with the plasma membrane is Mg2+-dependent and its activity is inhibited by Ca2+ at all concentrations studied. [32P]Phosphate is incorporated into phosphoserine and phosphothreonine. Only 13% of the incorporated 32P can be removed by washing the membranes in a high salt solution (0.5 m KCl). As resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis at pH 7.1, adenohypophyseal plasma membranes show a consistent pattern of 36 bands, of which 11 act as substrate for protein kinase. Cyclic adenosine 3' : 5'-monophosphate leads to a 40 to 100% increased incorporation of 32P into nine bands. Changes of the level of phosphorylation of components of the plasma membranes and of the membranes of the secretory granules could lead to altered rates of membrane fusion-fission processes accompanying exocytosis.
Free factories: from the quantum coreworld to the personal genome project (2009)

This dissertation develops technical and governance infrastructure for a by building on parallels with free and open source software and related communities. By viewing varied technologies and people as comprising free factories—or a federation of co-operating and competing factories with certain common ideals and infrastructure—I argue many scientific questions become easier to answer. 
In the first chapter, I briefly summarize the dissertation. I then describe the hardware, staff and other resources required to implement the computational aspects of a free factory with reasonable economies of scale. In the next chapter, I use the infrastructure to search for DNA and RNA editing events in more than 600 million genomic traces from ten organisms at NCBI. I find numerous examples of traces that support the existence of these phenomena and set the stage for a more comprehensive investigation. The subsequent chapter uses the same tools to analyze four individual human genomes for variants of clinical interest. This work demonstrates such analyses need not lead to costly or harmful medical workup. In the last chapter, I describe the initial data release of the Personal Genome Project. The release is derived from two gigabases of targeted sequence data from ten individuals. I investigate the quality of the data by comparison with Affymetrix 500K SNPs and discuss one variant of clinical interest. This data release—linking scientists, physicians and members of the general public—demonstrates the utility of free factories for advancing the state-of-the-art in personalized, genomic medicine. 
In Appendix A, I indicate how the Quantum Coreworld—earlier work on a digital evolution system consistent with the rules of quantum information processing—could efficiently use free factories. Such projects could allow free factories to fully utilize idle resources. Finally, in Appendix B, a novel, open-source primary data analysis pipeline is used to reprocess 100 gigabytes of image data derived from the exome of a Personal Genome Project participant. This approach demonstrates a 14% increase in placeable reads, on the PGP sample, over the vendor's pipeline.
Functional analysis of GAT-specific T cell clones: H-2-restricted monoclonal T helper cells do not regulate expression of antibody isotypes. (1982)

We obtained T cell clones specific for poly (Glu60, Ala30, Tyr10) (GAT) from GAT-primed lymph node cells of BALB/c mice. The clones consisted of helper cells that were carrier-specific and H-2-restricted and required a hapten-carrier bridge to activate B cells. They may be considered TH1 cells. They could all induce antibody responses of various isotypes in adoptive transfer in vitro. Isotypic patterns of the responses obtained with the clones were identical to those obtained with polyclonal T cells and were not dependent on the number of T helper cells added to the culture. Therefore, our observations demonstrate that classic TH1 cells do not regulate isotype expression on secondary responses. The expression of idiotype-like determinants on the GAT-specific clones was assayed. A syngeneic anti-idiotypic serum (B658), prepared in BALB/c mice against BALB/c anti-GAT antibodies previously characterized, was shown to block specifically the helper activity of GAT-specific T cell lines from BALB/c mice. Under the same experimental conditions the activity of none of the BALB/c clones was affected by serum B658.
Trend Detection in Control Data: Optimization and Interpretation of Trigg's Technique for Trend Analysis (1975)

A method for trend detection, Trigg's technique [Oper. Res. Q. 15, 271 (1964)], has been investigated for use in monitoring trends in control data produced by multitest continuous-flow analyzers. Simulated trend data were used to optimize the method. Actual control data were analyzed retrospectively to determine the frequency of trends and the accuracy of several parameters obtained from Trigg's method. The prospective use of the technique has successfully uncovered important trends. Criteria for the interpretation of the Trigg's trend data are suggested and an algorithm for the computer implementation of Trigg's calculations is included.
Epididymal sperm in assisted reproductive technology. (1992)

Infertile men with obstructive azoospermia mainly due to congenital absence of the vas deferens (CAVD) now have the option of trying to father their own progeny. In fact, in the last five years epididymal sperm retrieval microsurgically have been successfully used for in vitro fertilisation of human oocytes. In this report the clinical results of 98 consecutive procedures of microsurgical epididymal sperm aspiration (MESA) combined with in vitro fertilisation (IVF) and tubal embryo transfer (TET) are described. An overall fertilisation rate of 17% and a pregnancy rate of 36% per transfer is reported. Five of the 18 pregnancies resulted in abortion (27%) and 13 were delivered at term. Additionally, extra embryos for freezing and potential use for future attempts were made available for 13 couples. Men with CAVD have also allowed the study of spermatogenesis, immunological response and sperm disposal mechanisms in condition of chronic obstruction.
Ursodeoxycholyl Lysophosphatidylethanolamide Protects Against CD95/FAS-Induced Fulminant Hepatitis (2017)

Increased activation of CD95/Fas by Fas ligand in viral hepatitis and autoimmunity is involved in pathogenesis of fulminant hepatitis and liver failure. We designed a bile-acid phospholipid conjugate ursodeoxycholyl lysophosphatidylethanolamide (UDCA-LPE with LPE containing oleate at the sn-1) as a hepatoprotectant that was shown to protect against fulminant hepatitis induced by endotoxin. We herein further assessed the ability of UDCA-LPE to prevent death receptor CD95/Fas-induced fulminant hepatitis. C57BL/6 mice were intravenously administered with CD95/Fas agonistic monoclonal antibody (Jo-2) with or without 1 h pretreatment with 50 mg/kg UDCA-LPE. Jo-2 administration caused massive hepatocyte damage as seen by histology, and this was associated with a significant decrease in hepatic phosphatidylcholine (PC), lysoPC, and lysophosphatidylethanolamine levels. By histology, UDCA-LPE pretreatment improved hepatocyte damage and restored the loss of these phospholipids in part by a mechanism involving an inhibition of cytosolic phospholipaseA2 expression. Accordingly, Jo-2 treatment increased hepatic expression of cleaved caspase 8, caspase 3, and poly (ADP-Ribose) polymerase-1, and on the other hand decreased that of anti-apoptotic cellular FLICE-inhibitory protein. UDCA-LPE pretreatment was able to reverse all these changes. Moreover, UDCA-LPE attenuated inflammatory response by lowering the levels of Jo-2-induced proinflammatory cytokines TNF-α, IL-6, and IL-1β in liver and serum. UDCA-LPE was also able to decrease the levels of stimulated Th1/Th17 cytokines in Jo-2-primed isolated splenocytes. Taken together, UDCA-LPE exhibited potent anti-inflammatory effects against CD95/Fas-induced fulminant hepatitis.
Novel insights into negative pressure wound healing from an in situ porcine perspective (2021)

Negative pressure wound therapy (NPWT) is used clinically to promote tissue formation and wound closure. In this study, a porcine wound model was used to further investigate the mechanisms as to how NPWT modulates wound healing via utilization of a form of NPWT called the vacuum-assisted closure. To observe the effect of NPWT more accurately, non-NPWT control wounds containing GranuFoam™ dressings, without vacuum exposure, were utilized. In situ histological analysis revealed that NPWT enhanced plasma protein adsorption throughout the GranuFoam™, resulting in increased cellular colonization and tissue ingrowth. Gram staining revealed that NPWT decreased bacterial dissemination to adjacent tissue with greater bacterial localization within the GranuFoam™. Genomic analysis demonstrated the significant changes in gene expression across a number of genes between wounds treated with non-NPWT and NPWT when compared against baseline tissue. However, minimal differences were noted between non-NPWT and NPWT wounds, including no significant differences in expression of collagen, angiogenic, or key inflammatory genes. Similarly, significant increases in immune cell populations were observed from day 0 to day 9 for both non-NPWT and NPWT wounds, though no differences were noted between non-NPWT and NPWT wounds. Furthermore, histological analysis demonstrated the presence of a foreign body response (FBR), with giant cell formation and encapsulation of GranuFoam™ particles. The unique in situ histological evaluation and genomic comparison of non-NPWT and NPWT wounds in this pilot study provided a never-before-shown perspective, offering novel insights into the physiological processes of NPWT and the potential role of a FBR in NPWT clinical outcomes.
A printable form of single crystal silicon for high performance thin film transistors on plastic (2004)

This talk describes the fabrication and electrical characteristics of high performance thin film transistors derived from printed and solution cast micro/nanoscale objects of single crystal silicon. These elements are fabricated from conventional bulk silicon substrates or from silicon-on-insulator wafers by patterning a layer of resist by soft lithography, anisotropically wet etching the exposed silicon, and then lifting off the silicon. A large collection of such objects - which can have geometries that range from ribbons to platelets, sheets, disks and other shapes - constitutes a type of material, which we refer to as microstructured silicon (ps-Si), that can be deposited and patterned, by dry transfer printing or solution casting, onto plastic substrates to yield mechanically flexible thin film transistors that have excellent electrical properties.
Combining Refractive Solid Immersion Lens and Pulsed Laser Induced Techniques for Effective Defect Localization on Microprocessors (2008)

Abstract The spatial resolution and sensitivity of laser induced techniques are significantly enhanced by combining refractive solid immersion lens technology and laser pulsing with lock-in detection algorithm. Laser pulsing and lock-in detection enhances the detection sensitivity and removes the ‘tail’ artifacts due to amplifier ac-coupling response. Three case studies on microprocessor devices with different failure modes are presented to show that the enhancements made a difference between successful and unsuccessful defect localization.
The Detection of Ionizing Radiation by Plasma Panel Sensors: Cosmic\n Muons, Ion Beams and Cancer Therapy (2012)

The plasma panel sensor is an ionizing photon and particle radiation detector\nderived from PDP technology with high gain and nanosecond response.\nExperimental results in detecting cosmic ray muons and beta particles from\nradioactive sources are described along with applications including high energy\nand nuclear physics, homeland security and cancer therapeutics\n
Chemistry and Biology of a Series of Antitumor Sulfonamides: Exploiting Transcriptomic and Quantitative Proteomic Analyses for Exploring Druggable Chemical Space (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Design of Highly Integrated Mechatronic Gear Selector Levers for Automotive Shift-by-Wire Systems (2009)

Increased requirements regarding ergonomic comfort, limited space, weight reduction, and electronic automation of functions and safety features are on the rise for future automotive gear levers. At the same time, current mechanical gear levers have restrictions to achieve this. In this paper, we present a monostable, miniaturized mechatronic gear lever to fulfill these requirements for automotive applications. This solution describes a gear lever for positioning in the center console of a car to achieve optimal ergonomics for dynamic driving, which enables both automatic and manual gear switching. In this paper, we describe the sensor and actuator concept, safety concept, recommended shift pattern, mechanical design, and the electronic integration of this shift-by-wire system in a typical automotive bus communication network. The main contribution of this paper is a successful system design and the integration of a mechatronic system in new applications for optimizing the human-machine interface inside road vehicles.
High Spatial-Resoluation And Sensitivity Interferometric OTDR (1992)

Many kinds of silica-based glass waveguide circuits1 and LiNbO3 waveguides devices2 have been proposed. These devices are highly potential for optical communication systems and optical sensor systems. To develop these waveguide devices, a diagnosing system for detecting fault locations and characterizing them is necessary. The interferometric optical-time-domain reflectometer (OTDR) is promising to apply to diagnosing the optical devices, because of high spatial- resolution and high sensitivity compared with conventional OTDR systems. The interferometric OTDR was based on the Michelson interferometer using a low-coherent light source3. The reflectance profile inside the optical components is described by the distribution of the interferometric signal power between the reflection light from the scattering centers and the reference light.
Attenuation of methamphetamine‐induced neurotoxicity by selective sigma receptor ligands: in vivo and in vitro studies (2013)

Methamphetamine (METH) is one of the most widely abused illicit substances worldwide. It is capable of causing hyperthermia and neurotoxicity after high and/or repeated dosing. Selective ligands for sigma receptors were developed by our research team and shown in preclinical studies in male, Swiss Webster mice to significantly attenuate hyperthermia as well as several classical markers of METH neurotoxicity in the striatum: depletion of dopamine and 5‐HT levels, reductions in dopamine and 5‐HT transporter expression. Use of an NG108–15 cell culture model system to further delineate mechanisms underlying the protective effects of the sigma ligands reveals significant attenuation of METH‐induced ROS/RNS and caspase dependent pathways. In contrast, METH‐induced endoplasmic reticulum stress pathways are less affected by intervention with sigma ligands in NG108–15 cells. The relative contribution of each of the sigma receptor subtypes in the neuroprotective effects are still being elucidated, with preliminary data suggesting the importance of the sigma‐2 subtype. Together, the data indicate that sigma receptor ligands can intervene at numerous mechanisms that contribute to METH neurotoxicity. [Funding from NIDA: DA013978 , DA023205 ]
A Selective 3‐Acylation of Tetramic Acids and the First Synthesis of Ravenic Acid (2010)

3-Acyltetramic acids, including delicate 3-oligoenoyl derivatives, such as the Penicillium metabolite ravenic acid, were prepared in two high-yielding steps. Reaction of tetramic acids with the ylide Ph(3)PCCO afforded exclusively the corresponding 3-acylylidenetetramic acids. These were amenable to Wittig olefinations with aliphatic, aromatic, saturated and unsaturated aldehydes after deprotonation with KOtBu. Due to its simplicity, selectivity and tolerance of pH-sensitive groups this method is superior to the established acylation protocols by Jones and Yoshii. It is also applicable to the synthesis of 3-acyltetronic acids. The new 3-oligoenoyl tetramic acids exhibited structure-dependent antimicrobial and cytotoxic activity.
Design of a Soft Wearable Passive Fitness Device for Upper Limb Resistance Exercise (2022)

An increase in health awareness has fueled the development of fitness equipment or devices nowadays. Most conventional fitness devices have had some issues in space limitation and the high cost of equipment. With the advance in wearable robotics, we proposed a soft passive fitness wearable device for upper limb resistance exercises such as chest press, frontal raise, and chest fly. Users can customize the exercise intensity by adjusting the length of the elastic bands embedded in the wearable device. Moreover, the exer-tainment (Exercise-entertainment) user display interface was designed to motivate the user. Movements of users were estimated using inertial measurement units (IMUs), and haptic feedback was provided through the vibro-stimulation. Furthermore, the effectiveness of the proposed device was evaluated with the Borg scales representing the rating of perceived exertion (RPE) and measuring the surface electromyography (sEMG) of the three muscles located one on the shoulder and two on the chest. Both the Borg 6–20 and CR 10 scales were increased, and the normalized sEMG activities of the upper limb muscles with the activated device had more than double in magnitude compared to that with a bare condition; therefore, the proposed device has a potential effectiveness as for resistance exercise. Overall, this research devotes preliminary evidence on the benefits of the device in promoting the user to work out and contributing to the exercise effects.
Coordinated multi-point decoding with dual-polarized antennas (2011)

Coordinated multi-point processing has shown great potential for cellular networks, while multiple antenna systems (MIMO) is the key to next generation wireless communications. Full exploitation of MIMO technology, however, demands high antenna separation at the transceivers. This paper investigates the use of dual polarized antennas as a mean to overcome hardware size limitations. Uplink ergodic sum-rate capacity of a multicell joint processing (MJP) system employing dual polarized antennas is evaluated through theoretical analysis. Results are supported by numerical simulations. The designed system incorporates uniformly distributed users, path loss and Rayleigh fading, thus extending the well known Wyner model. Optimal and MMSE receiver architectures are compared in terms of capacity and complexity. System capacity is calculated with respect to cell size or cross polar discrimination (XPD). The results support the use of dual-polar decoding for low XPD, dense cellular systems while per polarization processing is acceptable in high XPD, sparse systems.
The Amphiphilic Properties of Spider Silks Are Important for Spinning (2007)

Along came a spider…︁ Spider silk is a fascinating biomaterial owing to its strength, extensibility, and toughness per unit weight which is unrivaled by man-made fibers. The spinning of spider silk corresponds to a transition from a liquid phase to a solid thread. The underlying mechanism of this transition has been investigated using a recombinantly produced spider silk protein.
A Study of Authentication in Daily Life. (2016)

We report on a wearable digital diary study of 26 participants that explores people’s daily authentication behavior across a wide range of targets (phones, PCs, websites, doors, cars, etc.) using a wide range of authenticators (passwords, PINs, physical keys, ID badges, fingerprints, etc.). Our goal is to gain an understanding of how much of a burden different kinds of authentication place on people, so that we can evaluate what kinds of improvements would most benefit them. We found that on average 25% of our participants’ authentications employed physical tokens such as car keys, which suggests that token-based authentication, in addition to password authentication, is a worthy area for improvement. We also found that our participants’ authentication behavior and opinions about authentication varied greatly, so any particular solution might not please everyone. We observed a surprisingly high (3–12%) false reject rate across many types of authentication. We present the design and implementation of the study itself, since wearable digital diary studies may prove useful for others exploring similar topics of human behavior. Finally, we provide an example use of participants’ logs of authentication events as simulation workloads for investigating the possible energy consumption of a “universal authentication” device.
Risk factors for loosening of cemented glenoid components in anatomical shoulder arthroplasty (2019)

Several risk factors leading to loosening of the glenoid have been described; however, there is no detailed information available on the exact numbers or percentages for each patient-related risk factor, implant-related risk factor, or risk factors related to surgical technique. Therefore, the aim of this multicenter study was to analyze these risk factors in a large cohort of patients treated with a 3rd-generation cemented total shoulder arthroplasty. Four-hundred seventy-one shoulder arthroplasties with a mean follow-up of 8.1 years were included. There were 318 women and 153 men. The mean age at the time of arthroplasty was 68 (range 35–90) years. The dominant shoulder was treated in 294 cases and the nondominant in 177. The following risk factors for loosening of the cemented keeled glenoid component were examined: gender, age, hand dominance, glenoid morphology, reaming on the glenoid side (reaming down the complete subchondral bone layer), glenohumeral mismatch, glenoid component design, and fatty degeneration of the rotator cuff. No influence on radiographic glenoid loosening was found for patient age at surgery, gender, hand dominance, preparation technique on the glenoid side, or fatty degeneration of the rotator cuff (p > 0.067). Excessive reaming on the native glenoid led to a 3.7-fold higher risk for glenoid component loosening (p < 0.001). A glenohumeral mismatch <6 mm was associated with higher radiographic loosening rates (p < 0.03). The use of a flat-back glenoid component led to a 3.1-fold higher risk for radiographic loosening compared to convex-back glenoids (p < 0.001). B2 glenoids had a higher risk for radiographic loosening compared to A1 (2.3-fold), A2 (3.6-fold), and B1 (2.7-fold) glenoids (p < 0.001). Based on a large and homogenous cohort of patients, this study has shown several risk factors for loosening of a cemented glenoid component in the midterm and long term. The loosening rates of cemented keeled glenoid components in primary osteoarthritis could possibly be reduced by optimizing surgical technique, implant configuration, and patient selection. Further long-term studies are necessary to confirm these findings.