gebhart/patrepeval huggingface dataset:
A high-flow Knudsen pump using a polymer membrane: Performance at and below atmospheric pressures (2010)

This paper describes a miniature gas (Knudsen) pump that utilizes thermomolecular flow through a nanoporous membrane. A temperature gradient along the length of a pore that supports free molecular gas flow at atmospheric pressure pumps gas molecules from the cold end to the hot end. In contrast with past work, the membrane material is mixed cellulose which provides superior uniformity in pore diameter and porosity. The final packaged volume of the Knudsen pump is 14×14×4.4 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . For an input power of 1.4 W, a single stage Knudsen pump based on these nanoporous polymer membrane has a temperature bias of 30 K across the thickness of the membrane, which provides 0.4 sccm flow against a 330 Pa pressure head. The load characteristics of the pump suggest that the pump can provide as much as 0.93 sccm gas flow in the absence of a load. Knudsen pump operation at sub-atmospheric pressures is also reported.
Supplementary Table S1 from Predicting Responses to Neoadjuvant Chemotherapy in Breast Cancer: ACRIN 6691 Trial of Diffuse Optical Spectroscopic Imaging (2023)

&lt;p&gt;Accrual table by institution.&lt;/p&gt;
Stability of UV-Type Two-Domain Wide-Viewing-Angle Liquid Crystal Display (1997)

We calculated the Gibbs free energy for the splayed-twist state, the reversed-twist state, and the reversed-tilt state of UV-type two-domain wide-viewing-angle thin film transistor liquid crystal display (TFT-LCD) panels to evaluate the stability of the three configurations. We show that the smaller tilt angle is the dominant fact on that influences the stability of the splayed-twisted state. Further more, at high applied voltage, the reversed-tilt state is the most unstable, and is easily deformed into the reversed-twist state. Methods are therefore proposed for reducing the reversed-tilt state area. General trends of the critical voltage as a function of the chiral pitch, twist angle, cell gap, dielectric constant, and elastic constant are also discussed.
2D material platform for overcoming the amplitude-phase tradeoff in ring modulators (2022)

Compact, high-speed electro-optic phase modulators play a vital role in various large-scale applications including phased arrays, quantum and neural networks, and optical communication links. Conventional phase modulators suffer from a fundamental tradeoff between device length and optical loss that limits their scaling capabilities. High-finesse ring resonators have been traditionally used as compact intensity modulators, but their use for phase modulation have been limited due to the high insertion loss associated with the phase change. Here, we show that high-finesse resonators can achieve a strong phase change with low insertion loss by simultaneous modulation of the real and imaginary parts of the refractive index, to the same extent i.e. $\frac{Δn}{Δk} \sim 1$. To implement this strategy, we utilize a hybrid platform that combines a low-loss SiN ring resonator with electro-absorptive graphene (Gr) and electro-refractive WSe$_2$. We achieve a phase modulation efficiency ($V_{\fracπ{2}} \cdot L_{\fracπ{2}}$) of 0.045 V $\cdot$ cm with an insertion loss (IL$_{\fracπ{2}}$) of 4.7 dB for a phase change of $\fracπ{2}$ radians, in a 25 $μ$m long Gr-Al$_2$O$_3$-WSe$_2$ capacitor embedded on a SiN ring of 50 $μ$m radius. We find that our Gr-Al$_2$O$_3$-WSe$_2$ capacitor can support an electro-optic bandwidth of 14.9 $\pm$ 0.1 GHz. We further show that the $V_{\fracπ{2}} \cdot L_{\fracπ{2}}$ of our SiN-2D platform is at least an order of magnitude lower than that of electro-optic phase modulators based on silicon, III-V on silicon, graphene on silicon and lithium niobate. This SiN-2D hybrid platform provides the impetus to design compact and high-speed reconfigurable circuits with graphene and transition metal dichalcogenide (TMD) monolayers that can enable large-scale photonic systems.
Live-cell imaging reveals the dynamics of PRC2 and recruitment to chromatin by SUZ12-associated subunits (2018)

Polycomb-repressive complex 2 (PRC2) is a histone methyltransferase that promotes epigenetic gene silencing, but the dynamics of its interactions with chromatin are largely unknown. Here we quantitatively measured the binding of PRC2 to chromatin in human cancer cells. Genome editing of a HaloTag into the endogenous <i>EZH2</i> and <i>SUZ12</i> loci and single-particle tracking revealed that ∼80% of PRC2 rapidly diffuses through the nucleus, while ∼20% is chromatin-bound. Short-term treatment with a small molecule inhibitor of the EED-H3K27me3 interaction had no immediate effect on the chromatin residence time of PRC2. In contrast, separation-of-function mutants of SUZ12, which still form the core PRC2 complex but cannot bind accessory proteins, revealed a major contribution of AEBP2 and PCL homolog proteins to chromatin binding. We therefore quantified the dynamics of this chromatin-modifying complex in living cells and separated the contributions of H3K27me3 histone marks and various PRC2 subunits to recruitment of PRC2 to chromatin.
Proto-dialytic cardiac function relates to intra-dialytic morbid events (2010)

Low CI and high TPRI in the first 30 min of HD are associated with an increased risk of IDME.
Inhibition of Human Dendritic Cell ER Stress Response Reduces T Cell Alloreactivity Yet Spares Donor Anti-tumor Immunity (2018)

Acute graft- vs. -host disease (GVHD) is an important cause of morbidity and death after allogeneic hematopoietic cell transplantation (HCT). We identify a new approach to prevent GVHD that impairs monocyte-derived dendritic cell (moDC) alloactivation of T cells, yet preserves graft- vs.-leukemia (GVL). Exceeding endoplasmic reticulum (ER) capacity results in a spliced form of X-box binding protein-1 (XBP-1s). XBP-1s mediates ER stress and inflammatory responses. We demonstrate that siRNA targeting XBP-1 in moDCs abrogates their stimulation of allogeneic T cells. B-I09, an inositol-requiring enzyme-1α (IRE1α) inhibitor that prevents XBP-1 splicing, reduces human moDC migration, allo-stimulatory potency, and curtails moDC IL-1β, TGFβ, and p40 cytokines, suppressing Th1 and Th17 cell priming. B-I09-treated moDCs reduce responder T cell activation via calcium flux without interfering with regulatory T cell (Treg) function or GVL effects by cytotoxic T lymphocytes (CTL) and NK cells. In a human T cell mediated xenogeneic GVHD model, B-I09 inhibition of XBP-1s reduced target-organ damage and pathogenic Th1 and Th17 cells without impacting donor Tregs or anti-tumor CTL. DC XBP-1s inhibition provides an innovative strategy to prevent GVHD and retain GVL.
PLGA-based nanomedicines manufacturing: Technologies overview and challenges in industrial scale-up (2021)

Nanomedicines based on poly(lactic-co-glycolic acid) (PLGA) carriers offer tremendous opportunities for biomedical research. Although several PLGA-based systems have already been approved by both the Food and Drug Administration (FDA) and the European Medicine Agency (EMA), and are widely used in the clinics for the treatment or diagnosis of diseases, no PLGA nanomedicine formulation is currently available on the global market. One of the most impeding barriers is the development of a manufacturing technique that allows for the transfer of nanomedicine production from the laboratory to an industrial scale with proper characterization and quality control methods. This review provides a comprehensive overview of the technologies currently available for the manufacturing and analysis of polymeric nanomedicines based on PLGA nanoparticles, the scale-up challenges that hinder their industrial applicability, and the issues associated with their successful translation into clinical practice.
Quantitative Disassembly and Reassembly of Human Papillomavirus Type 11 Viruslike Particles In Vitro (1998)

The human papillomavirus (HPV) capsid is primarily composed of a structural protein denoted L1, which forms both pentameric capsomeres and capsids composed of 72 capsomeres. The L1 protein alone is capable of self-assembly in vivo into capsidlike structures referred to as viruslike particles (VLPs). We have determined conditions for the quantitative disassembly of purified HPV-11 L1 VLPs to the level of capsomeres, demonstrating that disulfide bonds alone are essential to maintaining long-term HPV-11 L1 VLP structure at physiological ionic strength. The ionic strength of the disassembly reaction was also important, as increased NaCl concentrations inhibited disassembly. Conversely, chelation of cations had no effect on disassembly. Quantitative reassembly to a homogeneous population of 55-nm, 150S VLPs was reliably achieved by the re-formation of disulfide linkages following removal of reducing agent at near-neutral pH and moderate NaCl concentration. HPV-11 L1 VLPs could also be dissociated by treatment with carbonate buffer at pH 9.6, but VLPs could not be regenerated following carbonate treatment. When probed with conformationally sensitive and/or neutralizing monoclonal antibodies, both capsomeres generated by disulfide reduction of purified VLPs and reassembled VLPs formed from capsomeres upon removal of reducing agents exhibited epitopes found on the surface of authentic HPV-11 virions. Antisera raised against either purified VLP starting material or reassembled VLPs similarly neutralized infectious HPV-11 virions. The ability to disassemble and reassemble VLPs in vitro and in bulk allows basic features of capsid assembly to be studied and also opens the possibility of packaging selected exogenous compounds within the reassembled VLPs.
PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting (2019)

Plant-pathogenic Xanthomonas bacteria secrete transcription activator-like effectors (TALEs) into host cells, where they act as transcriptional activators on plant target genes to support bacterial virulence. TALEs have a unique modular DNA-binding domain composed of tandem repeats. Two amino acids within each tandem repeat, termed repeat-variable diresidues, bind to contiguous nucleotides on the DNA sequence and determine target specificity. In this paper, we propose a novel approach for TALE target prediction to identify potential virulence targets. Our approach accounts for recent findings concerning TALE targeting, including frame-shift binding by repeats of aberrant lengths, and the flexible strand orientation of target boxes relative to the transcription start of the downstream target gene. The computational model can account for dependencies between adjacent RVD positions. Model parameters are learned from the wealth of quantitative data that have been generated over the last years. We benchmark the novel approach, termed PrediTALE, using RNA-seq data after Xanthomonas infection in rice, and find an overall improvement of prediction performance compared with previous approaches. Using PrediTALE, we are able to predict several novel putative virulence targets. However, we also observe that no target genes are predicted by any prediction tool for several TALEs, which we term orphan TALEs for this reason. We postulate that one explanation for orphan TALEs are incomplete gene annotations and, hence, propose to replace promoterome-wide by genome-wide scans for target boxes. We demonstrate that known targets from promoterome-wide scans may be recovered by genome-wide scans, whereas the latter, combined with RNA-seq data, are able to detect putative targets independent of existing gene annotations.
Supplemental Figure 5 from MCL-1 Is a Key Determinant of Breast Cancer Cell Survival: Validation of MCL-1 Dependency Utilizing a Highly Selective Small Molecule Inhibitor (2023)

&lt;p&gt;Supplemental Figure 5: Flavopiridol synergizes with navitoclax in breast cancer cell lines &lt;sub&gt;in vitro.&lt;/sub&gt;&lt;/p&gt;
976. TLR and MyD88 Signaling Mediates Innate Immune Responses to Adenoviral Vectors in Mouse (2006)

Toxicity of adenoviral vectors induced after the acute interaction between the vector and innate immune system is the major hurdle for safe application of the vectors in humans. Toll-like receptors (TLRs) are the sentinels of innate immunity. We investigated the role of TLRs and the major TLR adaptor protein MyD88 in the host acute immune responses to systematic administration of type 5 adenoviral vectors. Following intravenous administration of E1E3- deleted Ad5-lacZ (2E11 pt./animal), a brisk accumulation of inflammatory cytokines including IL6, KC and TNF-α was found in the serum of C57B6 mice but remained barely detectable in that of MyD88 KO mice; the pattern of cytokine secretion in the splenic CD11c+ dendritic cells purified from the mice after vector administration appeared the same. CD11b immunostaining and neutrophil staining showed a robust infiltration of acute immune cells in liver while few were found in MyD88 KO mouse. Under the same vector treatment, secretion of acute cytokines such as KC and INFα were abolished in TLR2 KO mice while IL6 appeared slightly increased. Cytokine secretion in CD11c+dendritic cells from vector- injected TLR2 KO mice was further analyzed. Interactions between a panel of cloned TLRs (murine TLR1-9)/their dual combinations and Ad5 particles/purified capsid proteins were studied using in vitro cell-line cultures transfected with the receptor and NF-κB- driven luciferase reporter genes. Our results showed that UV- inactivated Ad5 particles induced activation of NF-κB signaling in CHO cells in the presence of TLR2 or TLR5, but not CAR receptor. Consistently we found Hexon protein purified from Ad5 activated NF-κB significantly in 293 cells in the presence of TLR2 orTLR5. Taken together, our data suggest that TLR and MyD88 signaling pathway(s) mediated the acute innate immune responses to Ad5 via direct interaction between TLRs and vector capsid proteins. Modification of the pathway may provide promising opportunities for the management of vector-associated toxicity and better application of the vectors.
Some Diesel Engine Sensors (1987)

&lt;div class="htmlview paragraph"&gt;Information Technology has affected the way we design and develop engines. The changes are due mostly to the availability of processing power. This will be used in a variety of ways in the future; this paper examines the effects which are likely or possible in Diesel engine control systems, especially in the sensors which provide their information. Emerging types of sensors are considered and some developments in the areas of cylinder pressure, combustion, gear meshing, engine torque and exhaust smoke are reviewed. The paper also speculates on the future development paths of control systems, for both short-term and long-term operation.&lt;/div&gt;
High Magnetoresistance Ratio and Low Resistance–Area Product in Magnetic Tunnel Junctions with Perpendicularly Magnetized Electrodes (2010)

We fabricated perpendicularly magnetized MgO-based magnetic tunnel junctions (p-MgO-MTJs) with a [Co/Pt]n/CoFeB/CoFe bottom electrode layer (free layer) and a CoFe/CoFeB/TbFeCo top electrode layer (reference layer). The insertion of thin CoFeB/CoFe layers at the barrier/electrode interfaces and post-annealing at a relatively low temperature of 225 °C simultaneously yielded high magnetoresistance (MR) ratios of up to 85% at room temperature and a low resistance–area (RA) product of 4.4 Ω µm2. Such a high MR ratio in low-RA p-MgO-MTJs is the key to developing ultrahigh-density spin-transfer-torque magnetoresistive random access memories (MRAMs).
Recent advances in audio and video text-to-speech synthesis (2001)

Harry Levitt characteristically combines a statistical or data-driven engineering approach with extensive scientific knowledge when tackling fundamental research questions (such as how to measure co-articulation) and practical problems (such as evaluating intelligibility). Some of Harry’s expansive research interests and contributions have focused on audio and video text-to-speech (TTS) synthesis. Some major recent improvements in these technologies that have resulted from applying similar approaches are discussed. The unit selection method of synthesis described differs from both the earlier techniques of formant synthesis and of concatenative synthesis from a diphone inventory. In unit selection synthesis, speech or video units are selected from among multiple candidates in a large database by optimizing a cost function. The cost functions used for unit selection are estimates of perceptual distances. The improvement in naturalness for both audio and visual TTS achieved through the unit selection technique is demonstrated, and some of its current limitations and future work needed in this area is discussed.
Machine learning using the extreme gradient boosting (XGBoost) algorithm predicts 5-day delta of SOFA score at ICU admission in COVID-19 patients (2021)

The XGBoost model predicted the change in SOFA score in critically ill COVID-19 patients admitted to the ICU and can guide clinical decision support systems (CDSSs) aimed at optimizing available resources.
P‐22: The Pixel Circuit of Out‐Pixel Compensation for LTPS PMOS OLED Displays (2019)

A 4T1C pixel circuit of out‐pixel compensation and the driving methods are proposed for LTPS PMOS OLED displays. The in‐pixel circuit is only to sense the characteristics of driving TFTs and write the driving voltage into its storage capacitor. The compensation is implemented by the out‐pixel circuits. The sensing period is separated from the driving period so that there is enough sensing time for the driving TFT to establish the stable sensing‐line voltage included the threshold voltage (V th ) information.
hTERT Inhibition Triggers Epstein–Barr Virus Lytic Cycle and Apoptosis in Immortalized and Transformed B Cells: A Basis for New Therapies (2013)

These results suggest that combination of antiviral drugs with strategies able to inhibit hTERT expression may result in therapeutically relevant effects in patients with EBV-related malignancies.
Does early initiation of ART in infants affect virological and resistance outcomes? Data from the CHER trial after 6 years of follow-up (2012)

Purpose of the study Virological outcomes and resistance patterns in children initiating protease inhibitor (PI)-based antiretroviral therapy (ART) immediately following HIV-1 diagnosis are not well described. Challenges include maintaining adherence in asymptomatic patients with very high pre-ART viral loads. The CHER trial compared deferred but continuous ART (arm 1) with early limited ART (arms 2 and 3).
Tumor-suppressive pathways in pancreatic carcinoma. (1997)

During tumorigenesis, positive selection is exerted upon those tumor cells that alter rate-limiting regulatory pathways. A corollary of this principle is that mutation of one gene abrogates the need for alteration of another gene in the same pathway and also that the coexistence in a single tumor of mutations in different genes implies their involvement in distinct tumor-suppressive pathways. We studied 42 pancreatic adenocarcinomas for genetic alterations in the K-ras oncogene and the p16, p53, and DPC4 tumor suppressor genes. All of them had the K-ras gene mutated. Thirty-eight % of the tumors had four altered genes, another 38% had three altered genes, 15% had two altered genes, and 8% of the tumors had one altered gene. Interestingly, we noted a high concordance of DPC4 and p16 inactivations (P = 0.007), suggesting that the genetic inactivation of p16 increases the selective advantage of subsequent mutation in DPC4. No statistically significant association was identified between the alteration of these cancer genes and pathological or clinical parameters. This type of multigenic analysis in human tumors may serve to substantiate experimental tumor models and thus increase our understanding of the truly physiologically relevant tumor-suppressive pathways that are abrogated during human tumorigenesis.
Cytosolic Phospholipase A2-A: A Potential TherapeuticTarget for Prostate Cancer (2008)

supply both cyclooxygenase and lipoxygenase pathways.We aim to determine the expression and activation of cPLA2-a in prostate cancer cell lines and tissue and the effect of targeting cPLA2-a in vitro and in vivo. Experimental Design:The expression of cPLA2-a was determined in prostate cancer cells by reverse transcription-PCR,Westernblot, and immunocytochemistry. Growth inhibition, apoptosis, and cPLA2-a activity were determined after inhibition with cPLA2-a small interfering RNA or inhibitor (Wyeth-1). Cytosolic PLA2-a inhibitor or vehicle was also administered to prostate cancer xenograft mouse models. Finally, the expression of phosphorylated cPLA2-awas deter-mined by immunohistochemistry in human normal, androgen-sensitive and androgen-insensitive prostate cancer specimens. Results: cPLA2-a is present in all prostate cancer cells lines, but increased in androgen-insensi-tive cells. Inhibitionwith small interfering RNA orWyeth-1results in significant reductions in pros-tate cancer cell numbers, as a result of reduced proliferation as well as increased apoptosis, and this was also associated with a reduction in cPLA2-a activity. Expression of cyclin D1and phos-phorylation of Akt were also observed to decrease.Wyeth-1inhibited PC3 xenograft growth by
Salvage of a Lower Extremity by Microsurgical Transfer of Tibial Bone From the Contralateral Extremity Traumatically Amputated at the Ankle Level (2009)

The authors present a case of free vascularized transfer of the tibial bone as an osteomyocutaneous flap based on the posterior tibial vessels. A 42-year-old man presented with severe crush injury to bilateral legs. The left tibial bone and soft tissue defect required reconstruction with an osteomyocutaneous free flap. Since the contralateral leg was traumatically amputated at the level of the ankle, a decision was made to harvest a free tibial osteomyocutaneous flap with below-knee-amputation completed. The transfer was achieved successfully with complete survival of the flap and bony union. This report describes the technical and healing aspects of such a unique transfer which may rarely be indicated.
Metastasis Upregulated Genes Have Distinct Function in C. elegans Cell Migrations (2014)

Cell migration is vital for normal animal development but also contributes to the invasive spreading of&#13;\nearly stage metastatic cancer. From two published databases, we complied 107 genes unregulated in&#13;\neither breast cancer or melanoma metastases and investigated their requirement in two Caenorhabditis&#13;\nelegans cell migrations: the male linker cell (LC) and hermaphrodite distal tip cells (DTC) which have&#13;\nsimilar functions as gonadal leader cells that undergo a complex migration while pulling non-motile&#13;\nfollowers. We performed an RNAi screen to identify genes implicated in normal LC and DTC migrations.&#13;\nThirty-two genes from the metastasis list were required for the cell migration of which 13 genes&#13;\neffected the migration of both LC and DTC, 18 genes effected only LC migration, and 4 genes only DTC&#13;\nmigration. The genes used by both cell types corresponded to genes involved in cell cycle activity,&#13;\nadhesion, cytoskeleton organization, protein degradation activity, spliceosome activity, ubiquitin-like&#13;\nmodification and function, and peptidase inhibition. The genes used by only the LC corresponded to&#13;\ngenes involved in adhesion, cytoskeletal organization, methyltransferase activity, metalloproteinase&#13;\nactivity, and signaling. Those genes used by only DTC corresponded to genes involved in signaling,&#13;\npeptidase inhibition, and utrophin activity. The significant differences among the developmental cell&#13;\nmigrations and the overlap in genes shared between the two metastases underscores the value of&#13;\ncharacterizing diverse genes and considering cell type in developing treatments.