gebhart/patrepeval huggingface dataset:
Millimeter wave-induced changes in membrane properties of leech Retzius neurons (2011)

This study evaluated a novel method for modulation of neuronal excitability using non-invasive delivery of millimeter waves. Millimeter waves at 60 GHz and incident power density of 100-600 &mu;W/cm<sup>2</sup> were applied to three intact segmental ganglia of the adult leach, and intracellular neuronal activity was recorded from the Retzius neurons using intracellular glass electrode. Transient dosedependent increase in the plasma membrane permeability was observed. In addition, in one of the examined neurons, a decrease in the neuronal firing rate was also evident. The results provide strong evidence for the feasibility of modulating neuronal excitability using non-invasive delivery of millimeter waves, and will be explored further for applications in basic neuroscience and treatment of neurological disorders.
Modeling and Simulation of Airflow Dynamics in a Dynamic Skip Fire Engine (2015)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Dynamic skip fire is a control method for internal combustion engines in which engine cylinders are selectively fired or skipped to meet driver torque demand. In this type of engine operation, fueling, and possibly intake and exhaust valves of each cylinder are actuated on an individual firing opportunity basis. The ability to operate each cylinder at or near its best thermal efficiency, and to achieve flexible control of acoustic and vibrational excitations has been described in previous publications.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Due to intermittent induction and exhaust events, air induction and torque production in a DSF engine can vary more than conventional engines on a cycle-to-cycle basis. This paper describes engine thermofluid modeling for this type of operation for purposes of air flow and torque prediction. Development of a one-dimensional model of medium complexity is described, along with solutions for practical issues encountered with the standard configuration of one-dimensional simulation packages such as GT-SUITE.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Airflow dynamic and thermodynamic simulation results for skip fire engine operation are presented and compared with experimental data under several different firing sequences. The dependence of air charge and net indicated mean effective pressure on skip fire sequence is illustrated.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Finally, a method of air estimation compensation is described via characterization of each induction event by skip history, both of the particular cylinder as well as previous cylinders in the firing order.&lt;/div&gt;&lt;/div&gt;
Electric Properties of Graphene-Based Conductive Layers from DC Up To Terahertz Range (2016)

This paper describes results obtained using a hybrid measurement methodology employed to investigate electric properties of thin conductive layers based on graphene nanoplatelets in the frequency band spanning from dc up to terahertz range. As many as four different measurement methods were employed to cover the band of interest, including the terahertz time-domain spectroscopy and the Fourier-transform infrared spectroscopy besides resonator techniques applicable in the microwave band and the four-point dc technique. Raw measurement data obtained using these approaches were processed and based on the results a relationship between frequency and sheet resistance for various types of new graphene-based conductive layers was extracted. Eventually, several models that help to explain the observed behavior of each of the analyzed conductive inks were proposed.
The role of gas phase reaction in the selective oxidation of methane (1988)

Partial oxidation of methane at 585 kPa and high temperature gives similar product yields in the presence and absence of catalysts indicating that the requirement for a suitable catalytic material is of secondary importance.
TSV/FET proximity study using dense addressable transistor arrays (2015)

Addressable transistor arrays (~20,000 devices) provide an attractive test vehicle to study TSV/FET proximity effects in a statistically meaningful way. FET/TSV proximity effect studies have been performed at the 45 nm node using a dense addressable parametric diagnostic (APD). We have found that a carefully designed TSV integration sequence at this node has minimal impact on the quality of devices. For the integration scheme studied, it was found that stress of the Si in the vicinity of the TSV had minimal impact on device characteristics for annular Cu TSVs, for devices placed as close as ~3μm to the TSV.
Covalent Docking in Drug Discovery: Scope and Limitations (2020)

Drug discovery efforts for new covalent inhibitors have drastically increased in the last few years. The binding mechanism of covalent compounds entails the formation of a chemical bond between their electrophilic warhead group and the protein of interest. The use of moderately reactive warheads targeting nonconserved nucleophilic residues can improve the affinity and selectivity profiles of covalent binders as compared to their non-covalent analogs. Recent advances have also enabled their use as chemical probes to disclose novel and also less tractable targets. Increasing interest in covalent drug discovery prompted the development of new computational tools, including covalent docking methods, that are available to predict the binding mode and affinity of covalent ligands. These tools integrate conventional non-covalent docking and scoring schemes by modeling the newly formed covalent bond and the interactions occurring at the reaction site. In this review, we provide a thorough analysis of state-of-the-art covalent docking programs by highlighting their main features and current limitations. Focusing on the implemented algorithms, we show the differences in handling the formation of the new covalent bond and their relative impact on the prediction. This analysis provides a comprehensive overview of the current technology and suggests future improvements in computer-aided covalent drug design. Finally, discussing successful retrospective and prospective covalent docking-based virtual screening applications, we intend to identify best practices for the drug discovery community.
Holistic UDAFs at streaming speeds (2004)

Many algorithms have been proposed to approximate holistic aggregates, such as quantiles and heavy hitters, over data streams. However, little work has been done to explore what techniques are required to incorporate these algorithms in a data stream query processor, and to make them useful in practice.In this paper, we study the performance implications of using user-defined aggregate functions (UDAFs) to incorporate selection-based and sketch-based algorithms for holistic aggregates into a data stream management system's query processing architecture. We identify key performance bottlenecks and tradeoffs, and propose novel techniques to make these holistic UDAFs fast and space-efficient for use in high-speed data stream applications. We evaluate performance using generated and actual IP packet data, focusing on approximating quantiles and heavy hitters. The best of our current implementations can process streaming queries at OC48 speeds (2x 2.4Gbps).
Ultrasensitive Circulating Tumor DNA Pilot Study Distinguishes Complete Response and Partial Response With Immunotherapy in Patients With Metastatic Renal Cell Carcinoma (2023)

In this pilot study, TARDIS accurately differentiated PR from CR among patients with mRCC receiving immunotherapy, and also prospectively identified patients at risk for subsequent progression. Given these findings, we envision subsequent studies that validate these results and investigate the utility of this assay to discern appropriate candidates for discontinuation of immunotherapy.
Experimental Demonstration of 84 Gb/s PAM-4 Over up to 1.6 km SSMF Using a 20-GHz VCSEL at 1525 nm (2017)

We demonstrate 84-Gb/s four-level pulse amplitude modulation (PAM-4) over up to 1.6-km standard single mode fiber using a 20-GHz single mode short cavity vertical cavity surface emitting laser diode at a transmission wavelength of 1525 nm. Different equalizer approaches including a common feedforward equalizer, a nonlinear Volterra equalizer (NLVE), a maximum likelihood sequence estimator (MLSE) and their combinations are evaluated working either as an equalizer for a standard PAM-4 or a partial response PAM-4 signal with seven levels. It is demonstrated that a standard FFE is not enough for a transmission distance of >0.6 km, while the use of an NLVE or FFE + MLSE is able to improve the transmission distance towards 1 km. The use of partial-response PAM-4 FFE in combination with a short memory MLSE is able to efficiently equalize the bandwidth limitations, showing more than 10-times BER improvement compared to standard NLVE or FFE + MLSE at a transmission distance of 1.6 km. Using a partial-response NLVE instead of an PR-FFE further performance improvement is achieved, resulting in BERs below the KP4 FEC-threshold with a BER-limit of 2E-4 after 1.6-km transmission distance, allowing error free operation.
Serpulina pilosicoli: a water-borne pathogen? (1997)

Serpulina pilosicoli is recognised as the causative agent of intestinal spirochaetosis (IS), a diarrhoeal disease which affects a variety of vertebrate hosts including pigs, dogs, birds and humans, It is commonly isolated from the faeces of individuals in developing communities, HIV positive patients and homosexual males in western societies. Additionally S. pilosicoli has been isolated from the bloodstream of debilitated patients. In order to determine the potential sources of human contamination, water from a lake at Perth Zoological Gardens and faeces from 43 water birds frequenting the lake were examined. S. pilosicoli was isolated and identified from eight of the 43 faecal samples (18.6%) and from three of the seven (42.8%) samples of lake water. A subset of 17 faecal samples were subjected to DNA extraction and PCR after primary culture, and eight (47%) were positive for S. pilosicoli DNA. Experimentally, S. pilosicoli was shown to survive in lake water for more than one month and in tap water for from one to 14 days. A volunteer who drank 1 x 10 9 cells of an S. pilosicoli strain mixed with tap water on three successive days became colonised with the same strain. The results suggest that water contaminated with faeces containing S. pilosicoli could be a source of infection for humans and animals.
Polymer optical interconnect technology (POINT): optoelectronic packaging and interconnect for board and backplane applications (1996)

The Polymer Optical Interconnect Technology (POINT) represents a major collaborative effort among GE, Honeywell, AMP, AlliedSignal, Columbia University and the University of California at San Diego (UCSD), sponsored by ARPA, in developing affordable optoelectronic module packaging and interconnect technologies for board- and backplane- level optical interconnect applications for a wide range of military and commercial applications. The POINT program takes a novel development approach by fully leveraging the existing electronic design, processing, fabrication and module packaging technologies to optoelectronic module packaging. The POINT program further incorporates several state-of-the-art optoelectronic technologies that include high-speed VCSEL for multichannel array data TM transmission; flexible optical polymers such as Polyguide or coupling of device-to-fiber using a passively alignment process; a low-loss polymer for backplane interconnect to provide a high I/O density; low-cost diffractive optical elements (DOE) for board-to-backplane interconnect; and use of molded MT array ferrule to reduce overall system size, weight, and cost. In addition to further reducing design and fabrication cycle times, computer simulation tools for optical waveguide and mechanical modeling will be advanced under the POINT program.
Abstract 12973: High-Intensity Focused Ultrasound (HIFU) Promotes Angiogenesis in a Rat Model of Peripheral Arterial Disease (2014)

Shock wave therapy (SWT) delivers single pulses of pressure to tissue, and promotes angiogenesis in animal models and humans with PAD and CAD. HIFU applies pulses of multiple pressure waves, which may be more efficient. We hypothesized that setting HIFU intensity to replicate peak negative pressures (-6 MPa) typically used for SWT would lead to greater angiogenesis. Eight week-old female Sprague-Dawley rats underwent left femoral artery excision to induce hindlimb ischemia, and the right hindlimb was used as an internal control. Rats were randomized to three groups (n=10 each): SWT (0.10 mJ/mm2), HIFU (1.054 MHz, 1 ms pulse duration), and sham therapy. Both treatments were applied at a pulse repetition frequency of 5 Hz, 200 pulses per spot, for six spots along the hindlimb. Rats were treated three times weekly for two weeks, and hindlimb perfusion was assessed with a Moor LDI Laser Doppler scanner. Compared with pre-treatment baseline (Fig 1A), HIFU improved the ratio of left:right perfusion by 23.6 ± 4.5% (mean ± SEM; Fig 1B), SWT by 17.0 ± 5.9%, and sham by 4.7 ± 3.4% (Fig 1C). Immunohistochemistry of gastrocnemius muscle was performed using anti-CD31 (PECAM) antibody, and microvascular density was quantified using ImageJ software. Both HIFU and SWT increased microvascular density in the left hindlimb (223 ± 4 and 217 ± 5 vessels/hpf, respectively) compared with sham (196 ± 7, p = 0.0001 for HIFU, p = 0.01 for SWT), but there was no significant difference between HIFU and SWT. RT-PCR was performed to examine the level of VEGF mRNA. HIFU increased left:right VEGF mRNA compared with sham (2.98 ± 0.69 vs 1.17 ± 0.23, p = 0.03), whereas SWT did not exhibit a significant change compared with sham (0.75 ± 0.20, p = 0.19). In conclusion, HIFU may be a potential non-invasive therapy for promotion of angiogenesis and reperfusion for PAD patients. Further research is needed to define a dose-response relationship of HIFU-mediated angiogenesis, and to elucidate its pro-angiogenic mechanisms.
Dynamic expressions of miR-34a and related target genes sirtuin 1 and nuclear factor-E2-related factor 2 and their significances in subependymal zone of rats with cerebral ischemia (2019)

Objective
To observe the expression changes of miR-34a and its related target genes sirtuin 1 (Sirt1) and nuclear factor-E2-related factor 2 (Nrf2) in subependymal zone (SVZ) of rats after cerebral ischemia, and to explore the effect of miR-34a on proliferation of endogenous neural stem cells (NSCs) after cerebral ischemia.


Methods
Forty SD rats were randomly divided into control group, cerebral ischemia one d group, cerebral ischemia three d group and cerebral ischemia 7 d group (n=10). Middle cerebral artery occlusion models were established by thread embolization in the latter three groups, and the SVZs were taken one, three and 7 d after model making, respectively. Immunofluorescence staining was used to detect the expression of nestin, real-time PCR was used to detect the mRNA expressions of miR-34a, Sirt1 and Nrf2, and Western blotting was used to detect the protein expressions of Sirt1 and Nrf2.


Results
(1) In SVZs of cerebral ischemia one d group, cerebral ischemia three d group and cerebral ischemia 7 d group, the number of nestin positive cells increased gradually ([2.013±0.526], [4.821±1.154], and [6.394±1.027]) cells/filed, with statistical differences (P< 0.05). (2) In SVZs of cerebral ischemia one d group, cerebral ischemia three d group and cerebral ischemia 7 d group, the expression levels of miR-34a mRNA increased gradually (0.295±0.145, 0.701±0.075, and 1.136±0.018), the Sirt1 mRNA expression levels showed a downward trend (0.835±0.024, 0.620±0.133, and 0.278±0.110), the Nrf2 mRNA expression levels obviously decreased (1.032±0.256, 0.833±0.187, and 0.630±0.123), the Sirt1 protein expression levels showed a downward trend (0.832±0.018, 0.731±0.156, and 0.454±0.132), and the Nrf2 protein expression levels obviously decreased (1.003±0.133, 0.813±0.111, and 0.671±0.071), with statistically significant differences (P<0.05). (3) Statistical correlation analysis showed that the number of nestin positive cells was positively correlated with miR-34a mRNA expression level and negatively correlated with Sirt1 and Nrf2 mRNA and protein expression levels after cerebral ischemia (r=0.887, P=0.003; r=-0.746, P=0.005; r=-0.521, P=0.013; r= -0.344, P=0.025; r=-0.863, P=0.000).


Conclusions
MiR-34a may regulate the proliferation of NSCs through Sirt1/Nrf2 pathway after cerebral ischemia.


Key words: 
Cerebral ischemia; MiR-34a; Sirtuin 1; Nuclear factor-E2-related factor 2; Neural stem cell; Cell proliferation
Comparison of Sexual Experience and Behavior between Bipolar Outpatients and Outpatients without Mood Disorders (2016)

Sexual behavior over the past year of 32 outpatients with Bipolar disorder is compared to that of 44 Comparison patients that had never had an episode of affective illness. Subjects were outpatients treated with drugs and psychotherapy in routine office practice. Differences in sexual behavior between the two groups as a whole were minimal, but meaningful differences emerged when subgroups were compared. Compared to control men, Bipolar men had had more partners in the last year and were more likely to have had sex without condoms. Compared to Bipolar females, Bipolar males had more sex partners, had more sex with strangers, and were more likely to have engaged in homosexual behavior. Even so, some patients in the Comparison group also had engaged in risky sexual behavior. They had failed to use condoms and had had sex with strangers and prostitutes during the previous year.
Detecting Canine Mastication: A Wearable Approach (2022)

Mastication is considered a coping mechanism in dogs, therefore, providing chew toys as an enrichment technique may be particularly important in stressful environments, such as the kennel. However, the relationship between chewing and welfare in kennel-housed dogs has not been systematically examined. The purpose of this study was to develop a sensor to quantify chewing with the intention that this technology could be used to understand the relationship between chewing and welfare in kennel-housed dogs. We show that a collar-based microphone can sense canine bites on a Nylabone chew toy. Four human raters annotated bites on audio samples collected from twelve dogs with five minutes of continuous access to the chew toy. A high degree of reliability was found with an average intraclass correlation coefficient (ICC) of 0.994. Using consensus labeling for training, we created bite detection algorithms using random forest, logistic regression, and convolutional neural network (CNN) based techniques. The CNN-based system achieved the highest performance recognition with an accuracy of 88% with a 91% F1 score. This technology will allow us to analyze a larger data set to uncover relationships between chewing styles and stress, cognition, and other characteristics associated with dog welfare.
Design of Area-Efficient, Robust and Reliable Junction Termination Extension in SiC Devices (2016)

This paper discusses SiC JTE design tradeoffs required to maximize device performance while minimizing consumed die area, fabrication cost and maintaining good reliability. Modeling and experimental results are provided.
Polycarbonates (2014)

Polycarbonates are an unusual and extremely useful class of polymers. The vast majority of polycarbonates are based on bisphenol A (BPA) and sold under the trade names Lexan, Makrolon, Calibre, and Panlite. BPA polycarbonates having high glass-transition temperatures are widely regarded for optical clarity and exceptional impact resistance and ductility at room temperature and below. Other properties such as modulus, dielectric strength, or tensile strength are comparable to other amorphous thermoplastics at similar temperatures below their respective glass-transition temperatures. Polycarbonates are prepared commercially by two processes: Schotten–Baumann reaction of phosgene and an aromatic diol in an amine-catalyzed interfacial condensation reaction, or via base-catalyzed transesterification of a bisphenol with a monomeric carbonate such as diphenyl carbonate. Important products are also based on polycarbonates in blends with other polymers, copolymers, branched resins, flame-retardant compositions, foams, and other materials. Polycarbonate, produced globally, has been the object of research studies, owing to its widespread utility and unusual properties. This article summarizes the preparation, properties, and utility of polycarbonates.
The proximal tubule and albuminuria: really! (2014)

Recent data highlight the role of the proximal tubule (PT) in reabsorbing, processing, and transcytosing urinary albumin from the glomerular filtrate. Innovative techniques and approaches have provided exciting insights into these processes, and numerous investigators have shown that selective PT cell defects lead to significant albuminuria, even reaching nephrotic range in animal models. Thus, the mechanisms of albumin reabsorption and transcytosis are undergoing intense study. Working in concert with megalin and cubilin, a nonselective multireceptor complex that predominantly directs proteins for lysosomal degradation, the neonatal Fc (FcRn) located at the brush border of the apical membrane has been implicated as the receptor mediating albumin transcytosis. The FcRn pathway facilitates reabsorption and mediates transcytosis by its pH-dependent binding affinity in endosomal compartments. This also allows for selective albumin sorting within the PT cell. This reclamation pathway minimizes urinary losses and catabolism of albumin, thus prolonging its serum half-life. It may also serve as a molecular sorter to preserve and reclaim normal albumin while allowing altered albumin to be catabolized via lysosomal pathways. Here, we critically review the data supporting this novel mechanism.
Life Science’s Average Publishable Unit (APU) Has Increased over the Past Two Decades (2016)

Quantitative analysis of the scientific literature is important for evaluating the evolution and state of science. To study how the density of biological literature has changed over the past two decades we visually inspected 1464 research articles related only to the biological sciences from ten scholarly journals (with average Impact Factors, IF, ranging from 3.8 to 32.1). By scoring the number of data items (tables and figures), density of composite figures (labeled panels per figure or PPF), as well as the number of authors, pages and references per research publication we calculated an Average Publishable Unit or APU for 1993, 2003, and 2013. The data show an overall increase in the average ± SD number of data items from 1993 to 2013 of approximately 7±3 to 14±11 and PPF ratio of 2±1 to 4±2 per article, suggesting that the APU has doubled in size over the past two decades. As expected, the increase in data items per article is mainly in the form of supplemental material, constituting 0 to 80% of the data items per publication in 2013, depending on the journal. The changes in the average number of pages (approx. 8±3 to 10±3), references (approx. 44±18 to 56±24) and authors (approx. 5±3 to 8±9) per article are also presented and discussed. The average number of data items, figure density and authors per publication are correlated with the journal's average IF. The increasing APU size over time is important when considering the value of research articles for life scientists and publishers, as well as, the implications of these increasing trends in the mechanisms and economics of scientific communication.