gebhart/patrepeval huggingface dataset:
The PKN1- TRAF1 signaling axis as a potential new target for chronic lymphocytic leukemia (2021)

TRAF1 is a pro-survival adaptor molecule in TNFR superfamily (TNFRSF) signaling. TRAF1 is overexpressed in many B cell cancers including refractory chronic lymphocytic leukemia (CLL). Little has been done to assess the role of TRAF1 in human cancer. Here we show that the protein kinase C related kinase Protein Kinase N1 (PKN1) is required to protect TRAF1 from cIAP-mediated degradation during constitutive CD40 signaling in lymphoma. We show that the active phospho-Thr774 form of PKN1 is constitutively expressed in CLL but minimally detected in unstimulated healthy donor B cells. Through a screen of 700 kinase inhibitors, we identified two inhibitors, OTSSP167, and XL-228, that inhibited PKN1 in the nanomolar range and induced dose-dependent loss of TRAF1 in RAJI cells. OTSSP167 or XL-228 treatment of primary patient CLL samples led to a reduction in TRAF1, pNF-κB p65, pS6, pERK, Mcl-1 and Bcl-2 proteins, and induction of activated caspase-3. OTSSP167 synergized with venetoclax in inducing CLL death, correlating with loss of TRAF1, Mcl-1, and Bcl-2. Although correlative, these findings suggest the PKN1-TRAF1 signaling axis as a potential new target for CLL. These findings also suggest the use of the orally available inhibitor OTSSP167 in combination treatment with venetoclax for TRAF1 overexpressing CLL.
Large-Scale Multi-Object Rearrangement (2019)

This paper describes a new robotic tabletop rearrangement system, and presents experimental results. The tasks involve rearranging as many as 30 to 100 blocks, sometimes packed with a density of up to 40%. The high packing factor forces the system to push several objects at a time, making accurate simulation difficult, if not impossible. Nonetheless, the system achieves goals specifying the pose of every object, with an average precision of ± 1 mm and ± 2°. The system searches through policy rollouts of simulated pushing actions, using an Iterated Local Search technique to escape local minima. In real world execution, the system executes just one action from a policy, then uses a vision system to update the estimated task state, and replans. The system accepts a fully general description of task goals, which means it can solve the singulation and separation problems addressed in prior work, but can also solve sorting problems and spell out words, among other things. The paper includes examples of several solved problems, statistical analysis of the system's behavior on different types of problems, and some discussion of limitations, insights, and future work.
Silicon Interposer Featuring Novel Electrical and Optical TSVs (2012)

Three-dimensional (3D) integrated circuits (ICs) yield system level performance improvements by providing high-bandwidth communication as well as opportunity for heterogeneous integration. It is envisioned that an area array of 3D stacked ICs can be interconnected using dense fine-pitch electrical and photonic interconnects on a silicon interposer. This paper presents a mechanically robust “thick” silicon interposer with novel electrical through-silicon vias (TSVs) and optical TSVs. The novel electrical TSVs described include polymer-clad TSVs and polymer-embedded vias. An advantage of using thick silicon interposer is that microchannels can be integrated in the thick silicon interposer to transfer a coolant to the 3D ICs with interlayer microfluidic heat sink or for the direct integration of a microfluidic heat-sink in the silicon interposer. However, as the thickness of silicon interposer increases, TSV electrical parasitics increase. Moreover, the coefficient of thermal expansion (CTE) mismatch between the copper TSV and silicon causes reliability issues. To reduce TSV capacitance as well as to reduce TSV stresses, polymer-clad electrical TSVs were fabricated. Using the same photodefinable polymer used for the cladding of electrical TSVs, optical TSVs were fabricated and characterized.
Cell volume changes in filtration studies of red cell deformability (1991)

We observed significant cell swelling in the Ringer's and tris based suspension media which can interfere with filtration studies of red cell deformability. Mean corpuscular volume (MCV) in Ringer's solution increased from 95.6±2.5 fl to 109.2±2.5 fl (N=5,P&lt;0.001) and from 95.4 fl±3.4 fl to 109.9±2.5 fl (N=5,P&lt;0.005) in tris-saline within 2 hours of preparation of the cell suspension. These alterations in cell volume were sufficient to cause significant increases in filtration time when using 3.0 um polycarbonate filters. At 30 mm Hg pressure gradient, Ringer's suspensions showed a three-fold increase in filtration time from 11.48±1.6 sec to 32.71±6.8 sec (N=5,P&lt;0.002), and in tris-saline, there was a six-fold increase in filtration time from 11.22±0.58 sec to 72.0±14.0 sec (N=5,P&lt;0.001). At 45 mm Hg, in Ringer's suspensions, filtration time increased from 9.03±1.40 sec to 19.48±1.31 sec (N=5,P&lt;0.001). These increases occured independent of hemolysis. Spontaneous cell swelling was prevented by using suspensions prepared with magnesium chloride and phosphate buffered saline. These experiments reveal that spurious changes in cell volume occur during filtration experiments using Ringer's and tris based suspension media and can confound the interpretation of deformability studies.
Genome-wide association study of susceptibility to idiopathic pulmonary fibrosis (2019)

Abstract Rationale Idiopathic pulmonary fibrosis (IPF) is a complex lung disease characterised by scarring of the lung that is believed to result from an atypical response to injury of the epithelium. The mechanisms by which this arises are poorly understood and it is likely that multiple pathways are involved. The strongest genetic association with IPF is a variant in the promoter of MUC5B where each copy of the risk allele confers a five-fold risk of disease. However, genome-wide association studies have reported additional signals of association implicating multiple pathways including host defence, telomere maintenance, signalling and cell-cell adhesion. Objectives To improve our understanding of mechanisms that increase IPF susceptibility by identifying previously unreported genetic associations. Methods and measurements We performed the largest genome-wide association study undertaken for IPF susceptibility with a discovery stage comprising up to 2,668 IPF cases and 8,591 controls with replication in an additional 1,467 IPF cases and 11,874 controls. Polygenic risk scores were used to assess the collective effect of variants not reported as associated with IPF. Main results We identified and replicated three new genome-wide significant ( P &lt;5×10 -8 ) signals of association with IPF susceptibility (near KIF15, MAD1L1 and DEPTOR) and confirm associations at 11 previously reported loci. Polygenic risk score analyses showed that the combined effect of many thousands of as-yet unreported IPF risk variants contribute to IPF susceptibility. Conclusions Novel association signals support the importance of mTOR signalling in lung fibrosis and suggest a possible role of mitotic spindle-assembly genes in IPF susceptibility.
ChemInform Abstract: First Stereoselective Synthesis of an Optically Pure β‐Substituted Histidine: (2S,3S)‐β‐Methylhistidine. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A comparative study of the clinical manifestations of systemic lupus erythematosus in Caucasians in Rochester, Minnesota, and Chinese in Singapore, from 1980 to 1992 (2001)

Chinese SLE patients are far less likely to have serositis or a hematologic disorder at diagnosis and may be more likely to develop proteinuria or CNS or other major organ involvement over the course of the disease, compared with Caucasian SLE patients. This may contribute to the increased mortality seen in Chinese SLE patients.
Optical waveguide modeling of refractive index mediated pH responses in silica nanocomposite thin film based fiber optic sensors (2016)

Recent experiments have demonstrated a pH-dependent optical transmission of silica based nanocomposite thin film enabled evanescent wave absorption spectroscopy based fiber optic sensors in aqueous solutions. Although the response was observed to linearly correlate with the pH-dependent surface charge density of the silica matrix, the responsible mechanism was not fully clarified. In this manuscript, an optical waveguide model is applied to describe observed responses through a modified effective refractive index of the silica matrix layer as a function of the solution phase pH. The refractive index dependence results from a surface charge dependent ionic adsorption, resulting in concentration of ionic species at charged surfaces. The resultant effective index modification to porous silica is estimated through effective medium theories and applied to an optical waveguide model of a multi-mode fiber optic based sensor response capable of reproducing all experimental observations reported to date.
Hybrid Backscatter and Relaying Scheme for 6G Greencom IoT Networks with SWIPT (2020)

&lt;div&gt;In order to support the massive number of resource-constrained Internet of Things (IoT) devices and machine-type devices, it is crucial to design future beyond 5G/6G wireless networks in an energy-efficient manner. To this end, this letter proposes a novel two-hop hybrid backscatter-and-relaying scheme to facilitate simultaneous wireless information and power transfer (SWIPT) considering both the Time-Switching (TS) and Power-Splitting (PS) receiver architectures, while dynamically modelling the involved dual-hop time-period (TP) metric. An optimization problem is formulated for the joint optimization of throughput, harvested energy, and transmit power of a SWIPT-enabled system with the proposed hybrid scheme, and is solved using a nonlinear optimizer. Our numerical results in terms of weighted utility function show the superior performance of proposed hybrid scheme over backscatter-only and relay-only schemes, while also depicting their individual performance benefits over the corresponding benchmark SWIPT systems designed with the fixed-TP.&lt;/div&gt;
Abstract 1115: Impaired Angiogenic Potential of Cardiac Progenitor Cells in Mice with a Cardiomyocyte-Restricted Knock Out of STAT3 (2007)

Mice with a cardiomyocyte-restricted knock out of STAT3 (KO: alpha-MHC-Cre tg/+; STAT3 flox/flox ) show a continuous decrease of the cardiac capillary density and develop heart failure beyond the age of 9 months. We sought to determine the paracrine influence of cardiomyocyte STAT3 on the endothelial differentiation potential of cardiac progenitor cells (CPC) of the adult mouse heart. Sca-1 + CPC were isolated from male mice hearts by MACS separation. STAT3 was entirely deleted in cardiomyocytes of KO mice, while CPC from KO showed normal expression of STAT3 (confirmed by PCR and Western blot). No difference in the total number of CPC per heart was observed between wildtype (WT: STAT3 flox/flox ) and KO mice. FACS analysis revealed a reduced number of endothelial progenitor cells (as defined by coexpression of Sca-1, CD31 and CD38, −25%, P&lt;0.05) among CPC from KO compared to CPC from WT. The differentiation potential of CPC from WT and KO was analyzed during in vitro culture on fibronectin-coated plates. After 4 weeks of culture RT-PCR for CD31 and immunohistochemistry (IHC) for endothelial cell (EC) marker tie2 and isolectin B4 was performed. CPC from WT showed markedly more efficient EC differentiation and tube formation compared to CPC from KO (p&lt;0.01). In contrast, adipocyte differentiation was enhanced in CPC from KO (p&lt;0.05, oil red staining and RT-PCR). Proliferation capacity of CPC from KO was reduced by 33% (p&lt;0.01) as compared to CPC from WT. Microarray results of freshly isolated CPC were consistent with the differences in EC and adipocyte differentiation (i.e. prostaglandin E receptor 3 up 2.3-fold in CPC from WT, Lipocalin-2 up 2.7-fold in CPC from KO). We did not observe cardiomyocyte differentiation (IHC for alpha-sarcomeric actinin; RT-PCR for Nkx 2.5, alpha-MHC, or alpha-skeletal actin) of CPC from both genotypes, neither in vitro by addition of oxytocin, 5-AZA, DMSO, nor following intramyocardial injection of CPC in vivo. Conclusion: STAT3-dependent paracrine mediators released from cardiomyocytes are determinants of differentiation and vasculogenic properties of new EC derived from cardiac progenitor cells. The identification of these factors may offer new approaches to enforce the endogenous vasculogenic repair potential of the adult heart.
Tell Me About Yourself (2020)

The rise of increasingly more powerful chatbots offers a new way to collect information through conversational surveys, where a chatbot asks open-ended questions, interprets a user’s free-text responses, and probes answers whenever needed. To investigate the effectiveness and limitations of such a chatbot in conducting surveys, we conducted a field study involving about 600 participants. In this study with mostly open-ended questions, half of the participants took a typical online survey on Qualtrics and the other half interacted with an AI-powered chatbot to complete a conversational survey. Our detailed analysis of over 5,200 free-text responses revealed that the chatbot drove a significantly higher level of participant engagement and elicited significantly better quality responses measured by Gricean Maxims in terms of their informativeness, relevance, specificity, and clarity. Based on our results, we discuss design implications for creating AI-powered chatbots to conduct effective surveys and beyond.
Erratum. Differential Health Care Use, Diabetes-Related Complications, and Mortality Among Five Unique Classes of Patients With Type 2 Diabetes in Singapore: A Latent Class Analysis of 71,125 Patients. Diabetes Care 2020;43:1048–1056 (2020)

An error occurred in the reporting of data in Table 2, “Health care use (yearly), incidence of diabetes-related complications from 2013 to 2016, …
Team Approach: Degenerative Spinal Deformity (2017)

➢ Degenerative spinal deformity is common and affects a large percentage of the aging population. The burden of degenerative spinal deformity is high when measured on the basis of prevalence, impact, and cost of care. ➢ A broad spectrum of specialists treat degenerative spinal deformities with use of both nonoperative and operative approaches to care. Treatment is characterized by substantial variability between and within specialties. Optimal care maximizes clinical benefit while limiting risks and costs. ➢ This review describes the case of a 68-year-old woman with symptomatic degenerative scoliosis and presents perspectives on management from specialists in physical therapy, pain management, neurosurgery, and orthopaedic surgery. ➢ The approaches to care presented here encompass a spectrum of risks, costs, and expected outcomes. Each specialist presents a perspective that is appropriate and reasonable, with its expected risks and benefits. ➢ The best approach is one that is not monolithic; collaboration between providers from multiple disciplines permits an approach to care that is responsive to the values and preferences of the individual patient. ➢ Clinical research, including prospective multidisciplinary comparative studies, is important for guiding an evidence-based approach to specific clinical scenarios and for developing a consensus regarding appropriate management strategies.
Effect of Erythropoietin on Erectile Function after Radical Prostatectomy: The ERECT Randomized Clinical Trial (2021)

In the context of brief perioperative dosing, erythropoietin did not improve recovery of erectile function for men undergoing radical prostatectomy for prostate cancer compared to placebo. Further research to identify effective adjuncts to improve health-related quality of life for these men is needed.
Persistent tachypnea of infancy is associated with neuroendocrine cell hyperplasia (2005)

We sought to determine the clinical course and histologic findings in lung biopsies from a group of children who presented with signs and symptoms of interstitial lung disease (ILD) without identified etiology. Patients were identified from the pathology files at the Texas Children's Hospital who presented below age 2 years with persistent tachypnea, hypoxia, retractions, or respiratory crackles, and with nonspecific and nondiagnostic lung biopsy findings. Age-matched lung biopsy controls were also identified. Their clinical courses were retrospectively reviewed. Biopsies were reviewed, and immunostaining with antibodies to neuroendocrine cells was done. Fifteen pediatric ILD patients and four control patients were identified for inclusion in the study. Clinically, the mean onset of symptoms was 3.8 months (range, 0-11 months). Radiographs demonstrated hyperinflation, interstitial markings, and ground-glass densities. Oxygen was initially required for prolonged periods, and medication trials did not eliminate symptoms. After a mean of 5 years, no deaths had occurred, and patients had improved. On review of the lung biopsies, all had a similar appearance, with few abnormalities noted. Immunostaining with antibodies to neuroendocrine cell products showed consistently increased bombesin staining. Subsequent morphometric analysis showed that immunoreactivity for bombesin and serotonin was significantly increased over age-matched controls. In conclusion, we believe this may represent a distinct group of pediatric patients defined by the absence of known lung diseases, clinical signs and symptoms of ILD, and idiopathic neuroendocrine cell hyperplasia of infancy. These findings may be important for the evaluation of ILD in young children.
Reduction of the thermal impedance of vertical-cavity surface-emitting lasers after integration with copper substrates (1996)

Vertical-cavity surface-emitting lasers (VCSELs) have been transferred from their original GaAs substrates to Cu substrates and continuous wave operation has been obtained on the VCSELs after epitaxial transfer. The resultant measurements show a doubling of the output power and a 20% reduction in the thermal impedance. Increased optical power is explained by improved thermal heat sinking as measured from the lasing spectra of horizontal-cavity edge-emitting lasers fabricated from the same VCSEL material.
Langmuir-Blodgett Films of a Functionalized Molecule with Cross-Sectional Mismatch Between Head and Tail (1994)

A functionalized surfactant has been investigated as floating monolayers by synchrotron x-ray diffraction and as bilayers transferred to solid supports by the Langmuir-Blodgett technique through atomic force microscopy. The transfer process is accompanied by an increase of the unit cell area (about 17 percent) and by an increase of the average domain diameter of nanometer-scale domains (about three times). The unit cell area of the floating monolayer corresponds to close packing of the head groups and a noncharacteristic packing of the tifted alkyl chains. The larger unit cell area of the bilayer film is consistent with a particular ordered packing of the alkyl chains, leaving free space for the head groups.
Effect of ginseng pretreatment on cerebral glucose metabolism in ischaemic rats using animal positron emission tomography (PET) and [18F]-FDG (1997)

To investigate the effect of ginseng on damaged brain activity, we evaluated the cerebral metabolic rate of glucose (CMRglc) as a functional index in post-ischaemic rats and compared the results with those obtained after the administration of a ginseng extract. CMRglc was measured using high resolution animal positron emission tomography with 18F-2-fluoro-2-deoxy-D-glucose (18F-FDG). The rats subjected to a 30-min occlusion showed a significant reduction of k3, the rate constant for phosphorylation of 18F-FDG by hexokinase, compared with the normal value. The ginseng pretreatment prevented the reduction in k3 and CMRglc caused by ischaemia. Although further investigation is needed to elucidate the mechanism of action, ginseng may be useful for prevention and treatment of ischaemia. © 1997 John Wiley & Sons, Ltd.
A Timely Administration of Antenatal Steroids Is Highly Protective Against Intraventricular Hemorrhage: An Observational Multicenter Cohort Study of Very Low Birth Weight Infants (2022)

Our observational data indicate that an ANS-birth interval of 24 h to 7 days is strongly associated with a reduced risk of intraventricular hemorrhage in VLBWIs. Further research is needed to improve the prediction of preterm birth in order to achieve a timely administration of antenatal steroids that may improve neonatal outcomes such as intraventricular hemorrhage.
Optically controlled photonic crystal nanocavity in silicon (2004)

We present experimental demonstration of fast all-optical switching in a one-dimensional photonic crystal nanocavity embedded in a Silicon waveguide. The transmission of the device is tuned by injecting free carriers into the nanocavity region using an optical pump beam. By strongly confining light in the photonic crystal nanocavity the sensitivity of light to small refractive index changes is enhanced. The small cavity volume (~0.1 &mu;m<sup>3</sup>) and unpassivated sidewalls enable ultra-fast switching speeds with low pulse energies. Using a pulse energy of only 60pJ, a refractive index change of approximately 10<sup>-2</sup> is obtained. This small index change, due to the high confinement nature of the cavity structure, leads to a strong change in transmission spectrum. Consequently, the resonance is shifted up to its full-width-at half-maximum (~7.5nm), and the transmission of the device is modulated by 71% with a time response of less than 1.5 ns. Such a device could open the door to the large-scale integration of ultra-fast modulators and switches.
Synthesis and characterization of surface patterned nanoimprinted in1–xCrxP/P(VDF‐TrFE) nanocomposite films for solar cell application potential (2017)

Nanoimprinted nanocomposites based on the inclusion of semiconductor quantum dots (QDs) into ferroelectric polymer matrix have shown a paramount encouragement owing to their versatile applications, such as field effect transistors, lasers, LEDs, bio‐probes, metal ion sensors, and photovoltaic devices. Here, we have developed a novel approach to fabricate nanoimprinted In 1– x Cr x P/P(VDF‐TrFE) nanocomposite films based on the nanoimprint lithography stamp technique for the first time. In 1– x Cr x P QDs have been prepared by colloidal technique at various contents of Cr ions from 1 at% to 9 at%. These QDs were doped into P(VDF‐TrFE). The prepared nanocomposite films were characterized by X‐ray diffraction, transmission electron microscopy, energy dispersive spectroscopy, Fourier transform spectroscopy, and atomic force microscopy. The thermal properties were investigated by thermogravimetric and differential scanning calorimetry. The inclusion of the In 1– x Cr x P QDs into the P(VDF‐TrFE) nanocomposites resulted in an enhancement of the thermal stability, an increase of the melting temperature and decrease of the Curie temperature. The nanoimprinted In 0.91 Cr 0.09 P/P(VDF‐TrFE) nanocomposite film showed high photocurrent response. The generated electromotive force, emf, in the nanoimprinted films was five times greater than the flat deposited film. Therefore, the developed surface pattern nanocomposite film based on In 1– x Cr x P/P(VDF‐TrFE) nanocomposite will open a new avenue for the flexible solar cell application potential. POLYM. COMPOS., 40:E136–E145, 2019. © 2017 Society of Plastics Engineers