gebhart/patrepeval huggingface dataset:
NMR Dipolar Cross-Relaxation Interaction Between Nanoconfined Fluids and Matrix Solids (2022)

Abstract Many different methods have been developed to investigate fluid-solid interactions in nanoporous systems. These methods either only work in the liquid phase or provide an indirect measurement by probing the fluid-solid interaction based on a measured property change of the fluid or solid under different sample conditions. Here, we report a direct measurement technique using NMR dipolar cross-relaxation between the nanoconfined fluids and the matrix solids. The method was tested using a methyl functionalized mesostructured silica saturated with methanol as a model sample. A formal theory was established to describe the enhanced dipolar cross-relaxation interaction between the nanoconfined fluids and the matrix solids. Both the experiment and theory showed that nanoconfinement of the fluids enhances the dipolar cross-relaxation interaction between the fluid and the matrix solids, which can be applied to investigate the fluid-solid interaction for various materials of similar nanostructure.
Non-thermal material and tissue processing with 100 MHz and 500 MHz repetition rate bursts (2013)

There are a number of applications that would avail a pulse pattern in the form of closely grouped and uniformly spaced pulses, i.e., bursts. Closely grouped pulses with pulse to pulse separation in the order of a few nanoseconds have a potential for increasing material removal rates and thereby reducing the thermal effects. Besides, keeping the burst repetition period in the order of thermal relaxation time has the advantage of keeping the overall average power at lower levels in order to prevent the cumulative heating of the material.
Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents (2023)

Several antibody therapeutics have been developed against SARS-CoV-2; however, they have attenuated neutralizing ability against variants. In this study, we generated multiple broadly neutralizing antibodies from B cells of convalescents, by using two types of receptor-binding domains, Wuhan strain and the Gamma variant as bait. From 172 antibodies generated, six antibodies neutralized all strains prior to the Omicron variant, and the five antibodies were able to neutralize some of the Omicron sub-strains. Structural analysis showed that these antibodies have a variety of characteristic binding modes, such as ACE2 mimicry. We subjected a representative antibody to the hamster infection model after introduction of the N297A modification, and observed a dose-dependent reduction of the lung viral titer, even at a dose of 2 mg/kg. These results demonstrated that our antibodies have certain antiviral activity as therapeutics, and highlighted the importance of initial cell-screening strategy for the efficient development of therapeutic antibodies.
MHRP: A Secure Multi-Path Hybrid Routing Protocol for Wireless Mesh Network (2007)

Wireless Mesh Network is a new and promising paradigm in wireless networks that allows network deployment at a much lower cost. Routing is the main research issue in the development of Wireless Mesh Networks. Many of the routing approaches have been borrowed from Wireless Mobile Ad hoc Network to achieve routing solutions in Wireless Mesh Networks but these approaches are not ideal or optimal. These routing protocols can be distinguished as proactive and reactive routing protocols. As a Wireless Mesh Network is itself a hybrid network solution among ad hoc and static networks, a hybrid routing approach is required. In this paper, we provide the secure multi-path version of this hybrid routing protocol, which enhances the reliability in the network, provide secure routing and has efficient techniques of finding alternate routes when a route is lost. We provide comparisons of this routing protocol with other routing protocols that are available for Wireless Mesh Networks.
Micro Quartz Tuning Fork-Based PM2.5 Sensor for Personal Exposure Monitoring (2018)

A portable, wireless, and cost-effective PM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.5</sub> sensor based on micro quartz tuning fork (MQTF) has been developed. Coated with repositionable polymer glue for effective absorption of PM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.5</sub> and with the help of innovative nozzle inlet, the MQTF-based sensor is highly sensitive to PM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.5</sub> in the detection range of 2 ~ 2000 μg/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> with high stability. The sensor response, change rate of the MQTF frequency, shows linear relationship with PM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.5</sub> concentration from 6 to 100 μg/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> at the flowrate of 1.7 L/min, which is a typical range of PM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.5</sub> concentration in ambient air. By integrating the repositionable adhesive coated MQTF, driving and detection circuit, PM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.5</sub> filter, sampling system, and a smartphone with Bluetooth and home-developed app, the MQTF-based sensor is assembled for personal PM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.5</sub> exposure monitoring. Furthermore, field tests show that the PM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2.5</sub> concentration readings from MQTF-based sensor and commercial PM monitor correlate very well with each other, which indicates the high accuracy and reliability of the MQTF-based sensor.
504 Specific in situ inflammatory architectures predict progression to renal failure in human lupus nephritis (2021)

<h3>Background</h3> In human lupus nephritis (LN), tubulointerstitial inflammation (TII) on biopsy predicts refractory disease and progression to end stage renal disease (ESRD). However, while approximately half of patients with moderate or severe TII develop ESRD, half do not. Therefore, we hypothesized that TII is heterogeneous with distinct inflammatory states each associated with different renal outcomes. <h3>Methods</h3> We interrogated renal biopsies from LN longitudinal (55 patients) and cross-sectional cohorts using both conventional and highly-multiplex (24 analytes) confocal microscopy. To accurately segment cells across whole biopsies, and to understand their spatial relationships, we trained and implemented a suite of computer vision tools, including multiple parallel Mask-R convolutional neural networks. This evolution of our previous analytic pipeline, Cell Distance Mapping (CDM)(<i>Nat Immunol</i>, 2019, 20:503), we refer to as CDM version 4. <h3>Results</h3> Across biopsies, B cell densities were strongly associated with protection from ESRD (p=2x10<sup>-8</sup>, Mann-Whitney). In contrast, CD4- T cell population densities, which included CD8, gd and double negative (CD4-CD8-, DN) T cells, predicted progression to ESRD (p=5.7x10<sup>-16</sup>). Breath first search and other analyses revealed inflammation was organized into different discrete niches each with unique characteristics including enrichment for specific cell populations. B cell were often organized into large clusters with CD4 T cells including T follicular helper-like cells. In contrast, the CD4- T cell populations formed small dispersed clusters which, on a per patient basis, predicted progression to ESRD (p=0.004). <h3>Conclusions</h3> These data reveal that in LN, specific <i>in situ</i> inflammatory states are associated with the failure of conventional therapy and progression to ESRD. <h3>Acknowledgments</h3> These studies were funded by the NIH Autoimmunity Centers of Excellence and Lupus Research Alliance.
Cooperative Caching for Chip Multiprocessors (2011)

Caching is widely used in computing and communication systems to improve data access efficiency. The main purpose of on-chip cache memory is to streamline processor operation by reducing the number of long-latency off-chip accesses. An ideal Chip Multiprocessors (CMP) caching scheme should be able to combine the strengths of different cache organizations and policies, and dynamically adapt to suitable behaviours to accommodate individual workload’s caching requirements. Cooperative caching uses cache partitioning to isolate workloads with weak locality from those with good locality and by integrating least recently used (LRU) replacement with cache partitioning. This chapter describes the uses in latency reduction and interference isolation and the three-layer model of complete complementary (CC) framework, the mechanism and implementation layers and the extension and implementation of CC for large-scale CMPs. It also describes three applications of CMP cooperative caching such as memory latency reduction, adaptive cache partitioning and cache performance isolation. Controlled Vocabulary Terms cache storage; multiprocessing systems; multiprocessor interconnection networks
High throughput intracellular delivery by viscoelastic mechanoporation (2023)

Brief and intense electric fields (electroporation) and/or tensile stresses (mechanoporation) have been used to temporarily permeabilize the plasma membrane of mammalian cells for the purpose of delivering materials to the cytosol. However, electroporation can be harmful to cells, while efficient mechanoporation strategies have not been scalable due to the use of narrow constrictions or needles which are susceptible to clogging. Here we report a method of mechanoporation in which cells were stretched and permeabilized by viscoelastic flow forces without surface contact. Inertio-elastic cell focusing aligned cells to the center of the device, avoiding direct contact with walls and enabling efficient (95%) intracellular delivery to over 200 million cells per minute. Functional biomolecules such as proteins, RNA, and ribonucleoprotein complexes were successfully delivered to Jurkat cells. Efficient intracellular delivery to HEK293T cells and primary activated T cells was also demonstrated. Contact-free mechanoporation using viscoelastic fluid forces appears to be feasible method for efficient and high throughput intracellular delivery of biomolecules to mammalian cells <i>ex vivo</i>.
Advances in the development and application of microbial consortia for metabolic engineering (2019)

Recent advances in metabolic engineering enable the production of high-value chemicals via expressing complex biosynthetic pathways in a single microbial host. However, many engineered strains suffer from poor product yields due to redox imbalance and excess metabolic burden, and require compartmentalization of the pathway for optimal function. To address this problem, significant developments have been made towards co-cultivation of more than one engineered microbial strains to distribute metabolic burden between the co-cultivation partners and improve the product yield. In this emerging approach, metabolic pathway modules can be optimized separately in suitable hosts that will then be combined to enable optimal functionality of the complete pathway. This modular approach broadens the possibilities to fine tune sophisticated production platforms and thus achieve the biosynthesis of very complex compounds. Here, we review the different applications and the overall potential of natural and artificial co-cultivation systems in metabolic engineering in order to improve bioproduction/bioconversion. In addition to the several advantages over monocultures, major challenges and opportunities associated with co-cultivation are also discussed in this review.
Dynamic Behavior of RS latches using FIB processing and probe connection. (2014)

Abstract. PUF (Physically Unclonable Function) technologies attract attention as a candidate to prevent counterfeit chips. A latch PUF is known as a high performance PUF among various types of proposed PUFs. In this paper we describe an experiment on a dynamic attack to a latch PUF consisting of RS latches, such as measuring the latch output by a probe connection after a FIB (Focused Ion Beam) processing. As a result, we conrmed that the latch PUF using the RS latch has a tolerance for the dynamic analysis, because the RS latch output was in uenced and changed by the FIB processing in our experiment. 1
Rat Strain Effects of AT 1 Receptor Activation on D 1 Dopamine Receptors in Immortalized Renal Proximal Tubule Cells (2005)

The dopaminergic and renin-angiotensin systems regulate blood pressure, in part, by affecting sodium transport in renal proximal tubules (RPTs). We have reported that activation of a D1-like receptor decreases AT1 receptor expression in the mouse kidney and in immortalized RPT cells from Wistar-Kyoto (WKY) rats. The current studies were designed to test the hypothesis that activation of the AT1 receptor can also regulate the D1 receptor in RPT cells, and this regulation is aberrant in spontaneously hypertensive rats (SHRs). Long-term (24 hours) stimulation of RPT cells with angiotensin II, via AT1 receptors increased total cellular D1 receptor protein in a time- and concentration-dependent manner in WKY but not in SHR cells. Short-term stimulation (15 minutes) with angiotensin II did not affect total cellular D1 receptor protein in either rat strain. However, in the short-term experiments, angiotensin II decreased cell surface membrane D1 receptor protein in WKY but not in SHR cells. D1 and AT1 receptors colocalized (confocal microscopy) and their coimmunoprecipitation was greater in WKY than in SHRs. However, AT1/D1 receptor coimmunoprecipitation was decreased by angiotensin II (10(-8) M/24 hours) to a similar extent in WKY (-22+/-8%) and SHRs (-22+/-12%). In summary, these studies show that AT1 and D1 receptors interact differently in RPT cells from WKY and SHRs. It is possible that an angiotensin II-mediated increase in D1 receptors and dissociation of AT1 from D1 receptors serve to counter regulate the long-term action of angiotensin II in WKY rats; different effects are seen in SHRs.
Loneliness and Diurnal Salivary Cortisol in Emerging Adults (2018)

This study aimed to examine the relationship between trait loneliness and diurnal rhythms of salivary cortisol. Fifty-One Chinese undergraduates provided six saliva samples on a weekday at immediately, 0.5, 3, 6, and 12 h after waking, and at bedtime. Saliva collection times were monitored using electronic devices (MEMS TrackCaps). Participants were also administered a questionnaire consisting of scales measuring, trait loneliness, depression, and demographics. Relationships between loneliness and the cortisol awakening response (CAR), diurnal slope (DS), and area under the curve with respect to ground (AUC<sub>G</sub>) were examined using multiple regression analyses. Results showed that a higher loneliness score was associated with an attenuated CAR, a large AUC<sub>G</sub>, and a steeper DS, with the effects of compliance, waking time, and depression being controlled. As a blunted CAR and a higher diurnal cortisol level have been shown to be associated with poorer health in prior studies, increased attention to the mechanisms translating loneliness into disease endpoints via elevated cortisol is warranted.
Ultrasensitive assay for saliva-based SARS-CoV-2 antigen detection (2021)

Abstract Widespread SARS-CoV-2 testing is highly valuable for identifying asymptomatic/pre-symptomatic individuals to slow community disease transmission. However, there remains a technological gap for highly reliable, easy, and quick SARS-CoV-2 diagnostic tests that are suitable for frequent mass testing. Compared to the conventional nasopharyngeal (NP) swab-based tests, saliva-based methods are attractive due to easier and safer sampling protocols. Despite its merits in rapid turn-around-time and high throughput compared to traditional PCR-based technologies, the widespread use of saliva-based SARS-CoV-2 rapid antigen tests is hindered by limited analytical sensitivity of current methods. Here, we report the first ultrasensitive, saliva-based SARS-CoV-2 antigen assay with an analytical sensitivity of &lt; 0.32 pg/ml, corresponding to 4 viral RNA copies/µl, which is comparable to that of PCR-based tests. Using the novel electrochemiluminescence (ECL)-based S-PLEX immunoassay, we measured the SARS-CoV-2 nucleocapsid (N) antigen concentration in 105 saliva samples obtained from non-COVID-19 and COVID-19 patients. Our assay displayed absolute specificity and high sensitivity (90.2%), where it correctly identified samples with viral loads up to 35 CT cycles by saliva-based PCR. Paired NP swab-based PCR results were also obtained for 86 cases for comparison. Our assay showed high concordance with saliva-based and NP swab-based PCR in samples with negative (&lt; 0.32 pg/ml) and strongly positive (&gt; 2 pg/ml) N antigen concentrations. Our study unveiled the ultrasensitivity and specificity of the saliva-based S-PLEX assay, demonstrating its clinical value as a high throughput, complementary alternative to PCR-based techniques. The novel technique is especially valuable in cases where compliance to frequent swabbing may be problematic (e.g. schools, nursing homes, etc.).
Pembrolizumab with chemotherapy, with or without bevacizumab for persistent, recurrent, or metastatic cervical cancer (2023)

In patients with progressive, recurrent, or metastatic PD-L1 expressing cervical cancer, without contraindication to anti-VEGF therapy, the use of pembrolizumab with bevacizumab and standard chemotherapy with carboplatin and paclitaxel is warranted. There is no evidence to support the use of pembrolizumab for this population broadly, and no evidence to support its use in PD-L1 non-expressing tumors.
Extracellular HIV‐1 Tat protein activates phosphatidylinositol 3‐ and Akt/PKB kinases in CD4+ T lymphoblastoid Jurkat cells (1997)

The biological basis for the pleiotropic activity of extracellular human immunodeficiency virus (HIV)-1 Tat protein on lymphoid T cell survival is not well understood. We have here demonstrated that the addition in culture of 0.1-10 nM Tat protein to 36-h serum-starved lymphoblastoid Jurkat T cells rapidly stimulates the catalytic activity of phosphatidylinositol 3-kinase (PI 3-K). The peak of activation was observed 30 min after Tat addition. Extracellular Tat also stimulated the catalytic activity of the Akt/PKB kinase, a major target of PI 3-K lipid products. Pretreatment of serum-starved Jurkat cells with 100 nM wortmannin (WT) or 10 microM LY294002, two unrelated pharmacological inhibitors of PI 3-K, markedly suppressed the catalytic activity of both PI 3-K and Akt/PKB in Jurkat cells. Moreover, at low concentrations (0.1-1 nM), extracellular Tat showed a small but reproducible protection of Jurkat cells from apoptosis induced by serum deprivation (p < 0.05), while the combination of Tat plus 100 nM WT significantly (p < 0.05) increased the percentage of apoptosis with respect to cells left untreated or treated with Tat alone. Taken together, these data suggest that the anti-apoptotic activity of low concentrations of Tat protein on Jurkat cells is mediated by a PI 3-kinase/Akt pathway.
High Fat Diet Causes Depletion of Intestinal Eosinophils Associated with Intestinal Permeability (2015)

The development of intestinal permeability and the penetration of microbial products are key factors associated with the onset of metabolic disease. However, the mechanisms underlying this remain unclear. Here we show that, unlike liver or adipose tissue, high fat diet (HFD)/obesity in mice does not cause monocyte/macrophage infiltration into the intestine or pro-inflammatory changes in gene expression. Rather HFD causes depletion of intestinal eosinophils associated with the onset of intestinal permeability. Intestinal eosinophil numbers were restored by returning HFD fed mice to normal chow and were unchanged in leptin-deficient (Ob/Ob) mice, indicating that eosinophil depletion is caused specifically by a high fat diet and not obesity per se. Analysis of different aspects of intestinal permeability in HFD fed and Ob/Ob mice shows an association between eosinophil depletion and ileal paracelullar permeability, as well as leakage of albumin into the feces, but not overall permeability to FITC dextran. These findings provide the first evidence that a high fat diet causes intestinal eosinophil depletion, rather than inflammation, which may contribute to defective barrier integrity and the onset of metabolic disease.
COVID-19 antibody therapeutics tracker: a global online database of antibody therapeutics for the prevention and treatment of COVID-19 (2020)

Facing the COVID-19 global healthcare crisis, scientists worldwide are collaborating to develop prophylactic and therapeutic interventions against the disease. Antibody therapeutics hold enormous promise for the treatment of COVID-19. In March 2020, the Chinese Antibody Society, in collaboration with The Antibody Society, initiated the "COVID-19 Antibody Therapeutics Tracker" ("Tracker") (https://chineseantibody.org/covid-19-track/) program to track the antibody-based COVID-19 interventions in preclinical and clinical development globally. The data are collected from the public domain and verified by volunteers on an ongoing basis. Here, we present exploratory data analyses and visualization to demonstrate the latest trends of COVID-19 antibody development, based on data for over 150 research and development programs and molecules included in the "Tracker" as of 8 August 2020. We categorized the data mainly by their targets, formats, development status, developers and country of origin. Although details are limited in some cases, all of the anti-SARS-CoV-2 antibody candidates appear to target the viral spike protein (S protein), and most are full-length monoclonal antibodies. Most of the current COVID-19 antibody therapeutic candidates in clinical trials are repurposed drugs aimed at targets other than virus-specific proteins, while most of these virus-specific therapeutic antibodies are in discovery or preclinical studies. As of 8 August 2020, eight antibody candidates targeting the SARS-CoV-2 S protein have entered clinical studies, including LY-CoV555, REGN-COV2, JS016, TY027, CT-P59, BRII-196, BRII-198 and SCTA01. Ongoing clinical trials of SARS-CoV-2 neutralizing antibodies will help define the utility of these antibodies as a new class of therapeutics for treating COVID-19 and future coronavirus infections.