gebhart/patrepeval huggingface dataset:
The Polycomb Group Protein EZH2 Impairs DNA Repair in Breast Epithelial Cells (2005)

The Polycomb group protein EZH2 is a transcriptional repressor involved in controlling cellular memory and has been linked to aggressive and metastatic breast cancer. Here we report that EZH2 decreased the expression of five RAD51 paralog proteins involved in homologous recombination (HR) repair of DNA double-strand breaks (RAD51B/RAD51L1, RAD51C/RAD51L2, RAD51D/RAD51L3, XRCC2, and XRCC3), but did not affect the levels of DMC1, a gene that only functions in meiosis. EZH2 overexpression impaired the formation of RAD51 repair foci at sites of DNA breaks. Overexpression of EZH2 resulted in decreased cell survival and clonogenic capacity following DNA damage induced independently by etoposide and ionizing radiation. We suggest that EZH2 may contribute to breast tumorigenesis by specific downregulation of RAD51-like proteins and by impairment of HR repair. We provide mechanistic insights into the function of EZH2 in mammalian cells and uncover a link between EZH2, a regulator of homeotic gene expression, and HR DNA repair. Our study paves the way for exploring the blockade of EZH2 overexpression as a novel approach for the prevention and treatment of breast cancer.
BISTs for post-bond test and electrical analysis of high density 3D interconnect defects (2018)

Cu-Cu hybrid bonding offers very high density interconnects (pitch around 2 μm or less) in 3D stacking integrated circuits (HD 3D-IC), but the smaller the Cu pad size, the more the fabrication and bonding defects have an important impact on yield and performance. Defects such as bonding misalignment, micro-voids and contact defects at the copper surface, can affect the electrical characteristics and the life time of 3D-IC considerably. In this paper, we propose two complementary test and characterization structures dedicated to high density 3D-IC interconnects. The first test structure permits to measure the misalignment defect with a great accuracy and the second to measure the RC delay of a periodic signal applied to a daisy chain composed of 3D Cu-Cu interconnects. The measured misalignment values and propagation delays allows to detect Cu-Cu full open, misalignment, and micro-voids, in order to assess performance of high density 3D Integrated Circuit. Both test structures are implemented as BIST engines, which are integrated and controlled with IEEE 1687, for an overall negligible area cost.
Effect ofChlamydia trachomatisInfection and Subsequent Tumor Necrosis Factor Alpha Secretion on Apoptosis in the Murine Genital Tract (2000)

The pathology observed during Chlamydia infection is due initially to localized tissue damage caused by the infection itself, followed by deleterious host inflammatory responses that lead to permanent scarring. We have recently reported that the infection by Chlamydia in vitro results in apoptosis of epithelial cells and macrophages and that infected monocytes secrete the proinflammatory cytokine interleukin-1beta. At the same time, proinflammatory cytokines such as tumor necrosis factor alpha (TNF-alpha) can also trigger apoptosis of susceptible cells. To study the possible relationship between Chlamydia trachomatis infection and apoptosis in vivo, we used the terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling technique to determine whether infection may cause apoptosis in the genital tract of mice and, conversely, whether cytokines produced during the inflammatory response may modulate the level of apoptosis. Our results demonstrate that infected cells in the endocervix at day 2 or 7 after infection are sometimes apoptotic, although there was not a statistically significant change in the number of apoptotic cells in the endocervix. However, large clumps of apoptotic infected cells were observed in the lumen, suggesting that apoptotic cells may be shed from the endocervix. Moreover, there was a large increase in the number of apoptotic cells in the uterine horns and oviducts after 2 or 7 days of infection, which was accompanied by obvious signs of upper tract pathology. Interestingly, depletion of TNF-alpha led to a decrease in the level of apoptosis in the uterine horns and oviducts of animals infected for 7 days, suggesting that the inflammatory cytokines may exert part of their pathological effect via apoptosis in infected tissues.
Design of a cooperative OFDM transceiver (2009)

We present the FPGA implementation of a MIMO and cooperative OFDM physical layer transceiver. Our transceiver is designed to support multiple antenna configurations, including SISO (single-antenna), receive switching diversity, transmit diversity using Alamouti's space-time block code and 2×2 spatial multiplexing. It also supports a fully-distributed physical layer cooperation scheme which allows two nodes to simultaneously transmit a common payload, achieving spatial diversity with only single-antenna transmissions. Our transceiver supports the common cooperative scheme of amplify-and-forward and provides a flexible interface for higher layers to enable cooperation as needed. The transceiver is implemented as a single FPGA core with a common datapath for all modes. This allows both efficient resource reuse between modes and a per-packet selection of antenna mode. This flexibility enables a wide variety of MIMO and cooperative protocols. We present architectural details of the cooperative transceiver design and early performance results using Rice University's Wireless Open-Access Research Platform (WARP).
ChemInform Abstract: REACTION OF TERT‐BUTYLCYANOKETENE WITH 2′‐CYCLOHEXYLSPIRO(FLUORENE‐9,3′‐OXAZIRIDINE) (1980)

Abstract Die Cycloaddition des Ketens (I) an das Oxaziridin (II) liefert die isomeren Produkte (III) und (IV).
A Randomized, Double‐Blind, Placebo‐Controlled Multicenter Study of Adalimumab in Pediatric Patients With Enthesitis‐Related Arthritis (2015)

Adalimumab reduced signs and symptoms of ERA at week 12, with improvement sustained through week 52. The safety profile was consistent with previous adalimumab studies.
Esculetin inhibits cell proliferation through the Ras/ERK1/2 pathway in human colon cancer cells (2010)

Esculetin, a phenolic compound, has been shown to inhibit the growth of colon tumors in animal studies. However, the roles of signaling pathways and cell cycle regulation in the esculetin-induced inhibition of cancer cell growth, remain to be elucidated. The present study suggests a novel mechanism for the Ras/ERK1/2 pathway in esculetin-treated human colon cancer HCT116 cells. The treatment of cells with esculetin resulted in significant growth inhibition and G1 phase cell cycle arrest, which led to the down-regulation of cyclin and cyclin-dependent kinase (CDK) expressions. This G1 phase cell cycle arrest was associated with the up-regulation of p27KIP expression. In addition, ERK1/2 was activated by esculetin. The pre-treatment of cells with the MEK1/2-specific inhibitor, PD98059, blocked the p27KIP expression induced by esculetin. Blockage of the ERK1/2 function consistently prevented the inhibition of cell proliferation and decreased G1 phase cell cycle protein levels. Furthermore, Ras activation was increased by the esculetin treatment. Transient transfection of the dominant negative Ras (RasN17) mutant gene abolished both the ERK1/2 activity and p27KIP expression induced by esculetin. Finally, the overexpression of RasN17 suppressed the esculetin-induced reduction in cell proliferation and cell cycle proteins. In conclusion, these results indicate that the Ras/ERK1/2 pathway is mediated by the p27KIP1 induction, leading to a reduction in cyclin/CDK complexes in the esculetin-induced inhibition of colon cancer cell growth. Overall, these findings indicate that the molecular action of esculetin has therapeutic potential for the treatment of colon malignancies.
ICT Requirements and Challenges for Provision of Grid Services from Renewable Generation Plants (2018)

The penetration of renewable energy into the electricity supply mix necessitates the traditional power grid to become more resilient, reliable and efficient. One way of ensuring this is to require renewable power plants to have similar regulating properties as conventional power plants and to coordinate their grid support services (GSS) as well. Among other requirements, the coordination of GSS will highly depend on the communication between renewable plants and system operators' control rooms, thereby imposing high responsibility on the under lying communication infrastructure. Despite such a widespread deployment, it is still neither completely known which communication technology solutions are currently in use, nor it is clear which of these technologies best fit to access and control these renewable plants in future. This is because of varying communication requirements for different GSS applications - in terms of data payloads, sampling rates, latency and reliability. Therefore, this paper presents a brief survey on the control and communication architectures for controlling renewable power plants in the future power grid, including the communication network technologies, requirements, and research challenges. To help identifying research problems in the continued studies, this paper attempts to ascertain how the underlying protocols in a communication stack influence timely and reliable communication in the said scenario.
Labeling of proteins and oligopeptides with luminescent lanthanide(III) chelates (2005)

Synthesis of a building block that allows introduction of photoluminescent europium(III) and samarium(III) chelates to synthetic oligopeptides on solid phase using standard Fmoc chemistry is described. Upon completion of the oligopeptide synthesis, these conjugates were converted to the corresponding lanthanide(III) chelates by treatment with appropriate lanthanide(III) salt. Also synthesis of a new terpyridine-based europium(III) chelate designed for solution phase protein labeling is demonstrated.
Molecular Electronic Tuning of Photosensitizers to Enhance Photodynamic Therapy: Synthetic Dicyanobacteriochlorins as a Case Study (2012)

Photophysical, photostability, electrochemical and molecular-orbital characteristics are analyzed for a set of stable dicyanobacteriochlorins that are promising photosensitizers for photodynamic therapy (PDT). The bacteriochlorins are the parent compound (BC), dicyano derivative (NC)2BC and corresponding zinc (NC)2BC-Zn and palladium chelate (NC)2BC-Pd. The order of PDT activity against HeLa human cancer cells in vitro is (NC)2BC-Pd > (NC)2BC > (NC)2BC-Zn ≈ BC. The near-infrared absorption feature of each dicyanobacteriochlorin is bathochromically shifted 35-50 nm (748-763 nm) from that for BC (713 nm). Intersystem crossing to the PDT-active triplet excited state is essentially quantitative for (NC)2BC-Pd. Phosphorescence from (NC)2BC-Pd occurs at 1122 nm (1.1 eV). This value and the measured ground-state redox potentials fix the triplet excited-state redox properties, which underpin PDT activity via Type-1 (electron transfer) pathways. A perhaps counterintuitive (but readily explicable) result is that of the three dicyanobacteriochlorins, the photosensitizer with the shortest triplet lifetime (7 μs), (NC)2BC-Pd has the highest activity. Photostabilities of the dicyanobacteriochlorins and other bacteriochlorins studied recently are investigated and discussed in terms of four phenomena: aggregation, reduction, oxidation and chemical reaction. Collectively, the results and analysis provide fundamental insights concerning the molecular design of PDT agents.
Development and characterization of a decellularised xenogeneic mitral valve scaffold (2014)

Mitral valve regurgitation is the second most common cause of surgery of the heart valves. Current treatment options are imperfect, requiring re-operations or lifelong anticoagulation therapy. The aim of this work was to develop and characterize a decellularised mitral valve scaffold for mitral valve replacement.
KoMBUS – MR-compatible ultrasound for improved biopsy needle guidance (2018)

Biopsies have become an essential tool for minimally invasive diagnostics and are part of the daily routine of interventional radiologists. Depending on the target organ that has to be sampled, different imaging modalities such as CT, ultrasound or MRI can be used. In particular, when it comes to detection of small tumors having a low contrast in ultrasound or CT, MRI is the method of choice. The risk for being off-target leading to a potentially false-negative diagnosis is reduced due to the better contrast on MR images. However, MRI still has drawbacks when compared to ultrasound with respect to cost issues, patient comfort and time-resolution.
Extended specifications and test data sets for data level comparisons of direct volume rendering algorithms (2001)

Direct volume rendering (DVR) algorithms do not generate intermediate geometry to create a visualization, yet they produce countless variations in the resulting images. Therefore, comparative studies are essential for objective interpretation. Even though image and data level comparison metrics are available, it is still difficult to compare results because of the numerous rendering parameters and algorithm specifications involved. Most of the previous comparison methods use information from the final rendered images only. We overcome limitations of image level comparisons with our data level approach using intermediate rendering information. We provide a list of rendering parameters and algorithm specifications to guide comparison studies. We extend Williams and Uselton's rendering parameter list with algorithm specification items and provide guidance on how to compare algorithms. Real data are often too complex to study algorithm variations with confidence. Most of the analytic test data sets reported are often useful only for a limited feature of DVR algorithms. We provide simple and easily reproducible test data sets, a checkerboard and a ramp, that can make clear differences in a wide range of algorithm variations. With data level metrics, our test data sets make it possible to perform detailed comparison studies. A number of examples illustrate how to use these tools.
Security vulnerability analysis of design-for-test exploits for asset protection in SoCs (2017)

SoCs implementing security modules should be both testable and secure. Oversights in a design's test structure could expose internal modules creating security vulnerabilities during test. In this paper, for the first time, we propose a novel automated security vulnerability analysis framework to identify violations of confidentiality, integrity, and availability policies caused by test structures and designer oversights during SoC integration. Results demonstrate existing information leakage vulnerabilities in implementations of various encryption algorithms and secure microprocessors. These can be exploited to obtain secret keys, control finite state machines, or gain unauthorized access to memory read/write functions.
Quantifying Composable Data Center Utilization (2022)

Composable data centers have been a strong topic of research interest, with potential benefits including higher resource utilization, faster and independent refresh cycles, flex-ible/optimum resource allocation and better capital and oper-ational costs. In this paper we use a discrete event simulation model to provide a quantitative assessment of the utilization ben-efits for a composable system versus conventional. We consider a simple multi-server loss queue situation as well as two more realistic scenarios: a mixed memory size demand and a mixed ratio CPU-GPU demand. In all these scenarios, composable systems can provide many tens of percent utilization advantage over more conventional hardware deployments. We also explore the impact of size of the composable resource pool on utilization.
Innovative printed circuit board technology for heat removal with application to power LED based operating room lamps (2009)

Using a simple analytical model we investigate the effect of thermal vias on the heat transfer through a printed circuit board (PCB) . We show that thermal vias can increase the heat transfer coefficient by orders of magnitude. The model considers the arrangement and the geometry of the vias, the metallization thickness and the solder fillets. The application part of the paper addresses three prototypes of high-power LED-based operating room lamps. The heat spreading ability of three types of PCBs - two FR4-based prototypes with thermal vias and one with an insulated metallic substrate (IMS) - is evaluated by using thermal simulation and single point temperature measurement with miniaturized thermocouples. All the three prototypes fulfilled the requirements for the thermal performance satisfactorily: the total thermal resistance of the FR4-based prototypes was below 1.2 K/W, and the one with the IMS even below 0.6 K/W.
Highly Diastereoselective Asymmetric Mannich Reactions of 1,3-Dicarbonyls with Acyl Imines (2006)

[reaction: see text] The cinchona alkaloids catalyze direct asymmetric Mannich reactions of cyclic 1,3-dicarbonyl compounds with acyl imines to afford alpha-quaternary carbon-bearing reaction products in yields of up to 98%, a diastereomeric excess of 90% or greater, and enantioselectivities up to 99% ee. A model is proposed that accounts for both the observed diastereoselectivities and the enantioselectivities for the reactions.
Polarization noise from forced vibration in a birefringent single-mode fiber link (1987)

Stable optical output from birefringent or polarization-preserving fibers is required in coherent optical communication and fiber-optic sensor systems. Fluctuations in the state of polarization (SOP) in birefringent fibers resulting from environmental conditions such as thermal drift and mechanical movement can induce intensity noise if polarization-dependent elements are included in the fiber link.1,3 The polarization noise originating from angular misalignment of the axes in the coupling of two birefringent fibers and/or the axes of the input fiber also has been discussed and analyzed.4
Meta-hologram-based authentication scheme employing a speckle pattern fingerprint (2020)

A concept for an optical holographic security tag is proposed and demonstrated. When illuminated with a laser beam, the image scattered from the tag projects a Quick Response code which encodes identifying information. The image also carries pseudorandom speckle noise, from which a unique speckle pattern "fingerprint" is derived. We show numerically that the tag is unclonable without access to a secret key - the starting conditions of the design algorithm. However, given the key, it is straightforward to reproduce a tag exhibiting the expected fingerprint. Several tags have been realized, implemented as plasmonic meta-holograms, and characterized experimentally. The robustness of the tag to fabrication error and its resilience to counterfeiting are studied in detail and demonstrated experimentally.
Bone Marrow-Derived Clonal Mesenchymal Stem Cells as a Source of Cell Therapy for Promoting Vocal Fold Wound Healing (2013)

BM-cMSCs appeared to survive in the injured xenogeneic VFs after transplantation for up to 1 month and favorably enhanced the wound healing of VFs after injury. We conclude that BM-cMSCs are a possible source of cell therapy for vocal fold regeneration.
A Tribute to Hans Dietrich Polaschegg (2013)

Roughly 60 years ago, we witnessed the birth of clinical dialysis. Since then we have celebrated many milestones and successes, as well as struggled with challenges. The first challenge, obviously, was in developing a system to cleanse uremic blood, which was made possible with the advent of dialysis in the 1950s. With the possibility to treat patients with end-stage renal disease a reality, the next obstacle was to make it available to the masses. By the end of the 1960s, this challenge was being met and a large population of uremic patients could receive dialysis treatment thanks to new technological advances. The trend continued in the 1970s, a decade which saw dialysis treatment become more reliable, comfortable, and safer with the advent of new blood pumps, accurate dialysis fluid modules, and disposable hemodialyzers. Treatment time could also be drastically cut from 12 to 4 h per session.By the mid-1980s, however, some significant challenges began to appear, especially concerning problems associated with long-term dialysis. One of these was hemodialysis-related amyloidosis, which highlighted the need for biocompatible high-flux membranes, pure or ultrapure dialysate, and personalized treatment. Technological advances, like the ultrafiltration control system for dialysis machines, and new approaches such as ‘treatment personalization’ and ‘treatment profiling’ helped to meet this new challenge.In looking back on this history of overcoming difficulties and mastering new challenges, one cannot help but to reflect upon Hans Dietrich Polaschegg (1942–2012), one of the major pioneers in the field of hemodialysis, who always advised against believing that there is nothing left to be done. After all, although challenges have been solved, just as many are probably right around the corner. And of course, the twenty-first century has already presented its first challenges. The medical community is having to tackle the problem of limited resources as health care plans struggle to contain costs across the board and emerging countries try to offer dialysis to their renal patients.Hans Dietrich Polaschegg was a major player in the field of hemodialysis and in many ways responsible for dialysis as we know it. He held over 100 patents, many of which were related to renal technology, and played a leading role in the development of technical and safety standards for dialysis equipment. After retiring as Head of Research and Development at Fresenius, Hans continued his research at home in his garage, at the University of Graz, and as a consultant. I had the privilege and honor of calling Hans a friend, and his charismatic personality had a strong impact on my professional, scientific, and private life. For this reason, I have been requested to deliver a memorial lecture and prepare a paper for this special issue of Blood Purification to pay tribute to and honor the memory of Hans Dietrich Polaschegg, his scientific knowledge, and his innovative spirit.Claudio Ronco, Vicenza
Flash vacuum pyrolysis of stabilised phosphorus ylides. Part 13.1 Extrusion of Ph3P from sulfinyl ylides and reactivity of the resulting sulfinyl carbenes (1998)

Six α-sulfinyl phosphorus ylides 6 have been prepared and are found upon flash vacuum pyrolysis at 500 °C to undergo mainly extrusion of Ph3P to give thioesters, presumably by 1,2-oxygen transfer in the initially formed sulfinyl carbenes; for α-arylsulfinyl ylides loss of Ph3PO to give additional products is also observed.