gebhart/patrepeval huggingface dataset:
UV laser-induced ferroelectric domain structures investigated by piezoresponse force microscopy (2007)

Ferroelectric domains have been generated on the +z and the <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> z faces of congruent undoped lithium niobate (LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ) single crystals by direct UV writing using a continuous wave (c.w.) frequency doubled argon ion laser (lambda=244 nm). The width of the domains was observed to depend on the intensity of the laser beam. Interestingly, also the contrast of the domains seen by piezoresponse force microscopy (PFM) was observed to increase with higher laser intensity. The contrast difference could be attributed to a difference of the depth of these surface domains as the depth sensitivity of the PFM is ~1 mum for LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> .
Development and Validation of a Multi-institutional Preoperative Nomogram for Predicting Grade of Dysplasia in Intraductal Papillary Mucinous Neoplasms (IPMNs) of the Pancreas (2016)

Objective: Previous nomogram models for patients undergoing resection of intraductal papillary mucinous neoplasms (IPMNs) have been relatively small single-institutional series. Our objective was to improve upon these studies by developing and independently validating a new model using a large multiinstitutional dataset. Summary Background Data: IPMNs represent the most common radiographically identifiable precursor lesions of pancreatic cancer. They are a heterogenous group of neoplasms in which more accurate markers of high-grade dysplasia or early invasive carcinoma could help avoid unnecessary surgery in 1 case and support potentially curative intervention (resection) in another. Methods: Prospectively maintained databases from 3 institutions were queried for patients who had undergone resection of IPMNs between 2005 and 2015. Patients were separated into main duct [main and mixed-type (MD)] and branch duct (BD) types based on preoperative imaging. Logistic regression modeling was used on a training subset to develop 2 independent nomograms (MD and BD) to predict low-risk (low- or intermediate-grade dysplasia) or high-risk (high-grade dysplasia or invasive carcinoma) disease. Model performance was then evaluated using an independent validation set. Results: We identified 1028 patients who underwent resection for IPMNs [MD: n = 454 (44%), BD: n = 574 (56%)] during the 10-year study period. High-risk disease was present in 487 patients (47%). Patients with high-risk disease comprised 71% and 29% of MD and BD groups, respectively (P <0.0001). MD and BD nomograms were developed on the training set [70% of total (n = 720); MD: n = 318, BD: n = 402] and validated on the test set [30% (n = 308); MD: n = 136, BD: n = 172]. The presence of jaundice was almost exclusively associated with high-risk disease (57 of 58 patients, 98%). Cyst size >3.0 cm, solid component/mural nodule, pain symptoms, and weight loss were significantly associated with high-risk disease. C-indices were 0.82 and 0.81 on training and independent validation sets, respectively; Brier scores were 0.173 and 0.175, respectively. Conclusions: For patients with suspected IPMNs, we present an independently validated model for the prediction of high-risk disease.
The Structural Basis for Substrate Anchoring, Active Site Selectivity, and Product Formation by P450 PikC (2006)

The pikromycin (Pik)/methymycin biosynthetic pathway of Streptomyces venezuelae represents a valuable system for dissecting the fundamental mechanisms of modular polyketide biosynthesis, aminodeoxysugar assembly, glycosyltransfer, and hydroxylation leading to the production of a series of macrolide antibiotics, including the natural ketolides narbomycin and pikromycin. In this study, we describe four x-ray crystal structures and allied functional studies for PikC, the remarkable P450 monooxygenase responsible for production of a number of related macrolide products from the Pik pathway. The results provide important new insights into the structural basis for the C10/C12 and C12/C14 hydroxylation patterns for the 12- (YC17) and 14-membered ring (narbomycin) macrolides, respectively. This includes two different ligand-free structures in an asymmetric unit (resolution 2.1 A ˚ ) and two co-crystal structures with bound endogenous substrates YC-17 (resolution 2.35 A ˚ )o r narbomycin (resolution 1.7 A ˚ ). A central feature of the enzymesubstrate interaction involves anchoring of the desosamine residue in two alternative binding pockets based on a series of distinct amino acid residues that form a salt bridge and a hydrogen-bonding network with the deoxysugar C3� dimethylamino group. Functional significance of the salt bridge was corroborated by site-directed mutagenesis that revealed a key role for Glu-94 in YC-17 binding and Glu-85 for narbomycin binding. Taken together, the x-ray structure analysis, site-directed mutagenesis, and corresponding product distribution studies reveal that PikC substrate tolerance and product diversity result from a combination of alternative anchoring modes rather than an induced fit mechanism. Macrolide antibiotics comprise a large group of medicinal agents characterized by a macrocyclic lactone ring, to which one or more sugar residues are covalently linked. Despite considerable structural variation, macrolides represent a homogeneous group of therapeutic drugs with similar activity spectra and mode of action as anti-infective agents. The success of macrolide antibiotics is attributed to their propensity to bind to the large subunit of prokaryotic ribosomes and inhibit protein synthesis, thereby preventing bacterial growth (1, 2). The first generation macrolide introduced into clinical practice over 50 years ago was erythromycin. Since then, macrolide antibiotics
Using crest lines to guide surface reconstruction from stereo (1996)

We propose an approach to interleave surface reconstruction from multiple images and feature extraction. It uses an object-centered representation that is optimized to conform to the surface shape. It also extracts typical features such as crest lines and uses them to guide the optimization. We present results using aerial images and terrain data.
A WLAN and bluetooth combo transceiver with integrated WLAN power amplifier, transmit-receive switch and WLAN/bluetooth shared low noise amplifier (2012)

A front-end circuit of a System-on-a-Chip (SoC) containing an IEEE 802.11b/g/n wireless LAN (WLAN) and a Bluetooth transceiver is presented. This SoC integrates a WLAN power amplifier (PA), a transmit-receive switch (T/R switch), a process and temperature insensitive power detector, and a low-noise amplifier (LNA) that is shared between WLAN and Bluetooth. The class AB power amplifier has a maximum saturated output power of +29dBm, while still meeting -28dB EVM for QAM64 modulation at an output power of +21dBm. The shared low-noise amplifier has a noise figure of 3.3dB. The presented solution significantly reduces the overall Bill-of-Materials (BOM) for the combo WLAN and Bluetooth transceivers.
Changes in gene body methylation do not correlate with changes in gene expression in Anthozoa or Hexapoda (2022)

Our results do not support the direct involvement of GBM in regulating dynamic transcriptional responses in invertebrates. If changes in DNA methylation regulate invertebrate transcription, the mechanism must involve additional factors or regulatory influences.
Tranexamic Acid Safely Reduced Blood Loss in Hemi- and Total Hip Arthroplasty for Acute Femoral Neck Fracture: A Randomized Clinical Trial (2017)

Therapeutic Level I. See Instructions for Authors for a complete description of levels of evidence.
High Sensitivity Protein Gel Electrophoresis Label Compatible with Mass-Spectrometry (2020)

Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is a widely utilized technique for macromolecule and protein analysis. While multiple methods exist to visualize the separated protein bands on gels, one of most popular methods of staining the proteins is with Coomassie dye. A more recent approach is to use Bio-Rad stain-free technology for visualizing protein bands with UV light and achieve similar or greater sensitivity than that of Coomassie dye. Here, we developed a method to further amplify the sensitivity of stain-free gels using carboxyfluorescein succinimidyl ester (CFSE) staining. We compared our novel method using foetal bovine serum samples with Coomassie dye, standard stain-free gels, and silver staining. Our results show that while silver staining remains a gold-standard method in terms of sensitivity; CFSE staining of samples prior to use with stain-free gels results in a 10-100-fold increase in sensitivity over Coomassie staining and the standard stain-free method. Our method offers a sensitivity similar to that of silver staining which is compatible with downstream mass spectrometry, and therefore more advantageous for further retrieval and analysis of macromolecules in bands.
Cancers as Wounds that Do Not Heal: Differences and Similarities between Renal Regeneration/Repair and Renal Cell Carcinoma (2006)

Cancers have been described as wounds that do not heal, suggesting that the two share common features. By comparing microarray data from a model of renal regeneration and repair (RRR) with reported gene expression in renal cell carcinoma (RCC), we asked whether those two processes do, in fact, share molecular features and regulatory mechanisms. The majority (77%) of the genes expressed in RRR and RCC were concordantly regulated, whereas only 23% were discordant (i.e., changed in opposite directions). The orchestrated processes of regeneration, involving cell proliferation and immune response, were reflected in the concordant genes. The discordant gene signature revealed processes (e.g., morphogenesis and glycolysis) and pathways (e.g., hypoxia-inducible factor and insulin-like growth factor-I) that reflect the intrinsic pathologic nature of RCC. This is the first study that compares gene expression patterns in RCC and RRR. It does so, in particular, with relation to the hypothesis that RCC resembles the wound healing processes seen in RRR. However, careful attention to the genes that are regulated in the discordant direction provides new insights into the critical differences between renal carcinogenesis and wound healing. The observations reported here provide a conceptual framework for further efforts to understand the biology and to develop more effective diagnostic biomarkers and therapeutic strategies for renal tumors and renal ischemia.
New hybrid core–shell star-like architectures made of poly(n-butyl acrylate) grown from well-defined titanium oxo-clusters (2011)

New hybrid star-like macromolecular objects have been designed from an inorganic multifunctional platform following two routes. The first one consists of the direct introduction of polymer arms at the surface of the titanium oxo-cluster [Ti16O16(OEt)32] by alkoxide exchange. The second approach corresponds to the growth by Atom Transfer Radical Polymerization (ATRP) of n-butyl acrylate from the macroinitiator [Ti16O16(OEt)26(OCH2CCl3)6]. By crossing different characterization techniques and methodologies (single crystal X-ray diffraction, 13C and 17O NMR and 1H DOSY NMR spectroscopy, Size Exclusion Chromatography), evidence of the formation of such macromolecular compounds is reported.
Exciton Confinement in Organic Multiple Quantum Wells (1995)

It has recently been shown that ordered, organic thin films of planar stacking molecules can be grown with monolayer uniformity and control over large substrate distances by the ultrahigh vacuum process of organic molecular beam deposition (OMBD). Due to this ability to grow films with such a high degree of order, it was demonstrated by So, et al 1 , 2 that multiple quantum well stacks consisting of alternating layers of the archetype compounds, 3,4,9,10 perylenetetracarboxylic dianhydridc (PTCDA) and 3,4,7,8 naphthalenetetracarboxylic dianhydride (NTCDA) exhibit exciton quantum confinement That is, energy shifts in the absorption spectrum, as well as time resolved photolumincscence indicates systematic changes with layer thickness, as the thickness is reduced from 500Å to 10Å. While these early data were compelling, they opened up many questions as to the nature of excitons in closely packed organic molecular systems. Hence, in this work, we have extended this early investigation by measuring the electroabsorption, the absorption and the fluorescence spectra of organic MQW stacks consisting of PTCDA+NTCDA, as well as 3,4,9,10 peryleneietracarboxylic-bis-benzimidazole (PTCBI)+NTCDA. These new investigations provide further information essential to understanding the nature of excitons in these van der Waals-bonded molecular solids.
The expression of nNOS, iNOS and nitrotyrosine is increased in the rat cerebral cortex in experimental hepatic encephalopathy (2006)

The changes in the distribution and amount of nitric oxide (NO) synthases (nNOS and iNOS) and the appearance of nitrotyrosine (NT) in the rat cerebral cortex were investigated following portacaval anastomosis (PCA), an experimental hepatic encephalopathy (HE) model. One month after PCA, rats showed more neurones immunoreactive to nNOS than did control animals. At 6 months post PCA, the number of neurones expressing nNOS had again increased and the intensity of the immunoreactions was stronger. Immunohistochemical analysis also showed that iNOS was increasingly expressed in pyramidal-like cortical neurones and in perivascular astrocytes from 1 to 6 months post PCA. In addition, a significant increase in cerebral iNOS concentration, at both post-PCA periods, was determined by Western blotting. The iNOS induction appears to be correlated with the length of the post-PCA period. PCA also induced the expression of NT, a nitration product of peroxynitrite. NT immunoreactivity was found in pyramidal-like cortical neurones. At 6 months, NT immunoreactivity was also evident in perivascular astrocytes, which was concomitant with a significant increase in NT protein level. PCA therefore not only increases the expression of nNOS but also induces the expression of iNOS and NT in both neurones and astrocytes. Taken together, these findings indicate that the induction of iNOS in pyramidal neurones and cortical astrocytes 6 months after PCA contributes to the generation of NT, and demonstrate the clear participation of NO in the pathogenic process of HE in this model.
Cryoprotectants & Cryopreservation of Equine Semen: A Review of Industry Cryoprotectants and the Effects of Cryopreservation on Equine Semen Membranes (2016)

Equine semen is a one of the most difficult in the industry to cryopreserve efficiently without causing damage to the membrane or apoptosis.This review consists of an in depth analysis of current cryoprotectant classes, membrane damage issues, reactive oxygen species generation, and apoptosis-all of which are exacerbated by cryopreservation.
Enhancing Channel Shortening Based Physical Layer Security Using Coordinated Multipoint (2021)

Wireless networks have become imperative in all areas of human life. As such, one of the most critical concerns in next-generation networks is ensuring the security and privacy of user data/communication. Cryptography has been conventionally used to tackle this, but it may not be scalable (in terms of key exchange and management) with the increasingly heterogeneous network deployments. Physical layer security (PLS) provides a promising alternative, but struggles when an attacker boasts a better wireless channel as compared to the legitimate user. This work leverages the coordinated multipoint concept and its distributed transmission points, in conjunction with channel shortening, to address this problem. Results show significant degradation of the bit-error-rate experienced at the eavesdropper as compared to state-of-the-art channel shortening-based PLS methods.
Co-regulated expression of dbl and poly(ADP-ribose) polymerase in Ewing's sarcoma cells and dbl-transformed NIH3T3 fibroblasts. (1995)

Poly(ADP-ribose) polymerase (PADPRP) is a ubiquitous enzyme constitutively expressed at low levels in the majority of eukaryotic cells, including most mammalian tumors and tumor-derived cell lines. Overexpression of PADPRP following the introduction of cDNA recombinant constructs into various cell types results in cell death. An exception to this effect are Ewing's sarcoma (ES) cells, which have been shown to contain elevated steady-state levels of PADPRP mRNA and high constitutive levels of protein and polymerase activity. In fact, this excess of PADPRP has been suggested to participate in the intrinsic radiosensitivity of Ewing's sarcomas, a highly malignant childhood bone tumor frequently curable with radiotherapy. It appears that ES cells might possess a hitherto unknown mechanism(s) by which PADPRP overexpression is controlled and made compatible with cell survival and proliferation. In order to investigate the contribution of other genetic alterations to PADPRP regulation in ES cells, we analysed the expression levels of PADPRP and of other genes, such as oncogenes and tumor suppressor genes, which may enhance the proliferative potential of ES cells. We have detected a positive correlation between the expression levels of the DNA-repair enzyme poly(ADP-ribose) polymerase and the dbl proto-oncogene in Ewing's sarcoma cells. The co-regulated expression of these genes has been established in NIH3T3 cells transformed by the human dbl oncogene or by overexpression of the dbl proto-oncogene. In both instances, the increase in dbl expression resulted in elevated levels of PADPRP mRNA and polymerase activity. The dbl oncogene was more efficient than the proto-oncogene in upregulating PADPRP expression. The inability of other oncogenes to upregulate PADPRP upon transformation of NIH3T3 cells demonstrated the specificity of the dbl in the process. Transfection of dbl-transformed NIH3T3 cells with retroviral PADPRP vectors resulted in the establishment of clones with PADPRP levels higher than those detectable in untransformed NIH3T3 cells transfected with the same retroviral constructs. These results suggest that dbl plays a role in the mechanism by which mammalian cells autoregulate their endogenous levels of PADPRP. Post-translational modification of the dbl or proto-dbl proteins by cytoplasmic PADPRP does not participate in the mechanism(s) underlying the observed PADPRP/dbl co-regulation.
Dietary isoflavones act on bone marrow osteoprogenitor cells and stimulate ovary development before influencing bone mass in pre‐pubertal piglets (2007)

Food containing soybeans provide isoflavone phytoestrogens that can preserve bone mass in postmenopausal women, and prevent bone loss in ovariectomized rats. But their effects on bone remain unclear, particularly on bone formation during growth. Two groups of eight pre-pubertal piglets were fed a basal or an isoflavone-enriched (S800) diet for 6 weeks. The S800 diet contained 800 mg SoyLifetrade mark/kg, providing 2.8 mg isoflavones/kg body weight/day. Several bones were collected and tested for bone strength and density. Bone marrow was collected from humeri together with blood samples and genital tracts. The plasma concentrations of isoflavones were increased in the pigs fed S800, but growth rate, body weight, plasma bone markers, bone mineral density, and strength were all unaffected. In contrast, cultured stromal cells from S800 pigs had more alkaline phosphatase-rich cells and mineralized nodules, secreted more osteocalcin, osteoprotegerin and RANK-L, synthesized more osteoprotegerin, and RANK-L. Cultured mononucleated nonadherent bone marrow cells from S800 pigs developed fewer tartrate-resistant acid phosphatase mononucleated cells (osteoclast progenitors) when cultured with 1,25(OH)(2)D(3), and resorbed a smaller area of dentine slices. Freshly isolated bone marrow osteoclast progenitors from S800 pigs had more caspase-3 cleavage activity, and synthesized less RANK. Both osteoclast and osteoblast progenitors had ERalpha and ERbeta, whose syntheses were stimulated by the S800 diet. The S800 piglets had heavier ovaries with more follicles, but their uterus weight was unaffected. We conclude that dietary isoflavones have no detectable effect on the bone mass of growing female piglets, but act on bone marrow osteoprogenitors via ERs--mainly ERbeta, and stimulate ovary development.
Introducing a silicone under the bump configuration for stress relief in a wafer level package (2004)

Microelectronics devices continue to evolve towards increased functionality, thinner die, increased reliability, and reduced cost, requiring a change in material and process requirements for the next generation of packages (i.e. stacked chip packages and wafer level packages (WLP)). Stress reduction is a key factor for many devices, particularly those that have thinner die and those that are subjected to stresses generated by thermal cycling. Wafer level packaging is an area where low stress and high volume manufacturing are critical for achieving good reliability and low manufacturing cost. Dow Coming and IMEC have been investigating a Silicone Under the Bump (SUB) wafer. level package as a potential route towards increased reliability. Including a SUB design into the device architecture provides a route to dissipate the stresses generated by the thermal expansion mismatch between the silicon die and the printed circuit board. Key to the device build is the application of a silicone pad using a photosensitive silicone or a screen printable silicone. In the design, metal traces from the bonding pads are redistributed to the tops of the silicone pads. Solder balls are placed on the metallized pads to complete the interconnection. The elastomeric nature of the pad dissipates the stresses created by the mismatch in CTE between the chip and the PCB and extends device reliability. To build the SUB enabled WLP device it was critical to understand the impact of the new materials on the device process steps. The uniqueness of the material set requires the creation and optimization of plasma cleaning processes specific to silicones, direct-on-silicone metallization and metal etching in the presence of silicones. The application of a solder mask and solder ball placement is required to complete a successful device build. In this paper we will discuss in detail the process steps utilized in building a silicone containing WLP. This will include a discussion on the process challenges including silicone pad integration, metallization, solder mask application and solder ball placement. The methodologies described in this paper can be generally applied for integration of photopatternable silicones into a range of devices and packages.
An Investigation of Low Frequency Plasma Instabilities in a Cylindrical Hollow Cathode Discharge (2014)

A new plasma-material interactions testbed (refered to as the Pi facility) is under development at UCLA, which uses a 250 A lanthanum hexaboride (LaB6) hollow cathode coupled to a cylindrical copper anode to provide a plasma environment representative of electric propulsion (EP) and pulsed power (PP) devices to a target material nearly 1 m downstream. A steady ion bombardment energy for long duration testing is desired, which requires a steady (known) plasma potential adjacent to the target. Time-resolved plasma potential measurements reveal oscillations of ∼20% of the discharge voltage occuring near the anode exit at a fundamental frequency of 10-20 kHz, which is between the local ion cyclotron and lower hybrid frequencies (fci < f < flh). A 70-90 kHz oscillation dominates on-axis and couples non-linearly with the m=1, fundamental mode and a ∼60 kHz fluctuation that is localized just off-axis. The present article investigates these oscillations through intrusive probing across a range of discharge paramaters.