gebhart/patrepeval huggingface dataset:
Non‐Melanoma Skin Cancers between the Years of 1990 and 1999 in Izmir, Turkey: Demographic and Clinicopathological Characteristics (2003)

The incidence of nonmelanoma skin cancers (NMSCs) has been rapidly increasing in epidemic proportions all over the world. The purpose was to evaluate the demographic and clinico-pathological patterns of skin cancers in Izmir, a region with high ultraviolet light exposure. The study was retrospective and hospital-based. The data related to all NMSC patients registered from January 1, 1990, to December 31, 1999, in the Dermatology Department of Ege University Medical School in Izmir, were collected and analyzed according to the personal statistics, anatomic location, dimensions of the lesion and clinical and histopathological type of skin cancer. A total number of 2,879 patients, aged between 20 and 96 years, were included in the study; among them 1,633 were men and 1,246 were women. The mean age of the patient population was 62.81 years, with a standard deviation of 12.50 years. Among the tumour patients, there were 2,062 basal cell carcinomas (BCCs), 746 squamous cell carcinomas (SCCs) and 71 both BCC and SCC; the total number of lesions was 3,186 (2,339 BCCs, 847 SCCs). Of all the NMSC lesions studied, the highest percentage (46.6%) were located on the face. For the BCCs, the most frequent histopathological subtype was the solid pattern (50.74%). The mean male: female ratios for SCC and BCC lesions were 2.86 and 1.01, respectively. Nodular and ulcerative forms (69.8%) were the most commonly found clinical types. Of all NMSCs, 78.4% had diameters in the 11 to 20 mm. BCC is the most common type of skin cancer diagnosed in our region. Among the NMSC patients, farming was the most widespread and risky job. The majority of SCC tumors were observed mostly in men 60 years old or above. This is the first comprehensive description of NMSCs in our region.
Intracellular localization of GBF proteins and blue light‐induced import of GBF2 fusion proteins into the nucleus of cultured Arabidopsis and soybean cells (1997)

The G-box is an important regulatory element found in the promoters of many different genes. Four members of an Arabidopsis gene family encoding basic leucine zipper proteins (GBFs) which bind the G-box have previously been cloned. To study GBFs, a polyclonal antibody was raised against GBF1 expressed in bacteria. This antibody also recognized GBF2 and GBF3. Immunoblot analysis of nuclear and cytoplasmic fractions from Arabidopsis and soybean (SB-M) cell cultures indicated that over 90% of proteins detected with anti-GBF1 were cytoplasmic. Electrophoretic mobility shift assays indicated that over 90% of G-box binding activity was cytoplasmic. DNA affinity chromatography demonstrated that each protein detected with anti-GBF1 specifically bound the G-box. To study individual GBFs, DNA constructs fusing GBF1, GBF2 and GBF4 to GUS were made and assayed by transient expression in SB-M protoplasts. Of GUS:GBF1 proteins, 50-62% were localized in the cytoplasm under all conditions tested, while 97% of GUS:GBF4 was localized in the nucleus. By contrast, whereas about 50% of GUS:GBF2 was found in the cytoplasm of dark-grown cells, over 80% of this protein was found in the nucleus in cells cultured under blue light. Deletion analysis of GBF1 identified a region between amino acids 112 and 164 apparently required for cytoplasmic retention. These results suggest the intriguing possibility that limitation of nuclear access may be an important control on GBF activity. In particular, GBF2 is apparently specifically imported into the nucleus in response to light.
CXCR4 Receptor Expression on Human Retinal Pigment Epithelial Cells from the Blood-Retina Barrier Leads to Chemokine Secretion and Migration in Response to Stromal Cell-Derived Factor 1α (2000)

Retinal pigment epithelial (RPE) cells form part of the blood-retina barrier and have recently been shown to produce various chemokines in response to proinflammatory cytokines. As the scope of chemokine action has been shown to extend beyond the regulation of leukocyte migration, we have investigated the expression of chemokine receptors on RPE cells to determine whether they could be a target for chemokine signaling. RT-PCR analysis indicated that the predominant receptor expressed on RPE cells was CXCR4. The level of CXCR4 mRNA expression, but not cell surface expression, increased on stimulation with IL-1beta or TNF-alpha. CXCR4 protein could be detected on the surface of 16% of the RPE cells using flow cytometry. Calcium mobilization in response to the CXCR4 ligand stromal cell-derived factor 1alpha (SDF-1alpha) indicated that the CXCR4 receptors were functional. Incubation with SDF-1alpha resulted in secretion of monocyte chemoattractant protein-1, IL-8, and growth-related oncogene alpha. RPE cells also migrated in response to SDF-1alpha. As SDF-1alpha expression by RPE cells was detected constitutively, we postulate that SDF-1-CXCR4 interactions may modulate the affects of chronic inflammation and subretinal neovascularization at the RPE site of the blood-retina barrier.
Electrophysiological correlates of episodic migraine chronification: evidence for thalamic involvement (2013)

Our results show abnormalities in chronic migraine that are also reported during attacks in episodic migraineurs, namely early response sensitization and late habituation. The HFO analysis suggests that this sensory sensitization may be explained by an increase in the strength of the connections between the thalamus and cortex compared to episodic migraine between attacks. Whether this electro-functional behaviour is primary or secondary to daily headache, thus reflecting an electrophysiological fingerprint of the somatosensory system central sensitization process, remains to be determined.
Small Molecule Inhibitors Induce Conformational Changes in the I Domain and the I-like Domain of Lymphocyte Function-associated Antigen-1 (2002)

The beta(2) integrin lymphocyte function-associated antigen-1 (LFA-1) is a conformationally flexible alpha/beta heterodimeric receptor, which is expressed on the surface of all leukocytes. LFA-1 mediates cell adhesion crucial for normal immune and inflammatory responses. Intracellular signals or cations are required to convert LFA-1 from a nonligand binding to a ligand binding state. Here we investigated the effect of small molecule inhibitors on LFA-1 by monitoring the binding of monoclonal antibodies mapped to different receptor domains. The inhibitors were found to not only induce epitope changes in the I domain of the alpha(L) chain but also in the I-like domain of the beta(2) chain depending on the individual chemical structure of the inhibitor and its binding site. For the first time, we provide strong evidence that the I-like domain represents a target for allosteric LFA-1 inhibition similar to the well established regulatory L-site on the I domain of LFA-1. Moreover, the antibody binding patterns observed in the presence of the various inhibitors establish a conformational interaction between the LFA-1 I domain and the I-like domain in the native receptor that is formed upon activation. Differentially targeting the binding sites of the inhibitors, the L-site and the I-like domain, may open new avenues for highly specific therapeutic intervention in diseases where integrins play a pathophysiological role.
Noninvasive magnetic resonance thermography of soft tissue sarcomas during regional hyperthermia (2006)

Noninvasive MR thermography of soft tissue sarcoma was feasible and suitable for validating the quality of heating during RHT.
North East Italian Prospective Hospital Renal Outcome Survey on Acute Kidney Injury (NEiPHROS-AKI) (2007)

Acute kidney injury (AKI) in the intensive care unit (ICU) is associated with an enhanced mortality. The Acute Dialysis Quality Initiative group has proposed the RIFLE (Risk-Injury-Failure-Loss-ESRD) classification to standardize the approach to AKI. This study was performed to estimate the AKI incidence in ICU patients in northeastern Italy and describe clinical characteristics and outcomes of patients with AKI on the basis of their RIFLE class. A prospective multicenter observational study was performed of patients who fulfilled AKI criteria in 19 ICU in northeastern Italy. Data were analyzed using multivariate logistic regression and survival curve analysis. Of 2164 ICU patients who were admitted during the study period, 234 (10.8%; 95% confidence interval 9.5 to 12.1%) developed AKI; 19% were classified as risk (R), 35% as injury (I), and 46% as failure (F). Preexisting kidney disease was present in 36.8%. The most common causes of AKI were prerenal causes (38.9%) and sepsis (25.6%). At diagnosis of AKI, median serum creatinine and urine output were 2.0 mg/dl and 1100 ml/d, respectively. ICU mortality was 49.5% in class F, 29.3% in I, and 20% in R. Independent risk factors for mortality included RIFLE class, sepsis, and need for renal replacement therapy, whereas a postsurgical cause of AKI, exposure to nephrotoxins, higher serum creatinine, and urine output were associated with lower mortality risk. In this study, AKI incidence in the ICU was between 9 and 12%, with 3.3% of ICU patients requiring renal replacement therapy. Sepsis was a significant contributing factor. Overall mortality was between 30 and 42%, and was highest among those in RIFLE class F.
Seven Research Challenges of Generalized 3D Documents (2007)

The rapid evolution of information and communication technology has always been a source for challenging new research questions in computer science. The vision of the emerging research field of semantic 3D is to establish the notion of generalized 3D documents that are full members of the family of generalized documents. This means that access would be content-based rather than based on metadata. The purpose of this article is to highlight the research issues that impede the realization of this vision today. The seven research challenges include: (1) '3D data set' can have many meanings, (2) a sustainable 3D file format, (3) representation-independent stable 3D markup, (4) representation-independent 3D query operations, (5) documenting provenance and processing history, (6) consistency between shape and meaning, and (7) closing the semantic gap
all sewn up! (2014)

Accountant Deborah Wood pieces together the essential pattern to forming a federation
Molecular cloning and sequencing of cDNAs encoding the entire rat fatty acid synthase. (1989)

Overlapping cloned cDNAs representing the entire sequence of the rat fatty acid synthase mRNA have been isolated from a cDNA library and sequenced. Authenticity of the cDNA clones was supported by hybridization to fatty acid synthase mRNA and by amino-terminal sequencing of 39 fatty acid synthase CNBr fragments. The full-length fatty acid synthase mRNA is 9156 nucleotides long and includes an 84-nucleotide 5' noncoding region, a 7515-nucleotide coding sequence, and a 1537-nucleotide 3' noncoding region; a second mRNA species containing a shortened 3' noncoding sequence is also transcribed in the rat. The encoded fatty acid synthase subunit contains 2505 amino acids and has a molecular weight of 272,340. Active sites and substrate binding sites were located within the sequence, thus establishing the order of domains on the multifunctional animal fatty acid synthase as condensing enzyme-transferase-dehydrase-enoyl reductase-ketoreductase-acyl carrier protein-thioesterase.
Contributions of Primate Prefrontal and Posterior Parietal Cortices to Length and Numerosity Representation (2009)

The ability to understand and manipulate quantities ensures the survival of animals and humans alike. The frontoparietal network in primates has been implicated in representing, along with other cognitive abilities, abstract quantity. The respective roles of the prefrontal and parietal areas and the way continuous quantities, as opposed to discrete ones, are represented in this network, however, are unknown. We investigated this issue by simultaneously analyzing recorded single-unit activity in the prefrontal cortex (PFC) and the fundus of the intraparietal sulcus (IPS) of two macaque monkeys while they were engaged in delayed match-to-sample tasks discriminating line length and numerosity. In both areas, we found anatomically intermingled neurons encoding either length, numerosity, or both types of quantities. Even though different sets of neurons coded these quantities, the representation of length and numerosity was similar within the IPS and PFC. Both length and numerosity were coded by tuning functions peaking at the preferred quantity, thus supporting a labeled-line code for continuous and discrete quantity. A comparison of the response characteristics between parietal and frontal areas revealed a larger proportion of IPS neurons representing each quantity type in the early sample phase, in addition to shorter response latencies to quantity for IPS neurons. Moreover, IPS neurons discriminated quantities during the sample phase better than PFC neurons, as quantified by the receiver operating characteristic area. In the memory period, the discharge properties of PFC and IPS neurons were comparable. These single-cell results are in good agreement with functional imaging data from humans and support the notion that representations of continuous and discrete quantities share a frontoparietal substrate, with IPS neurons constituting the putative entry stage of the processing hierarchy.
A cloning method for caspase substrates that uses the yeast two-hybrid system: Cloning of the antiapoptotic gene gelsolin (1998)

Caspase-mediated proteolysis is a critical and central element of the apoptotic process; therefore, it is important to identify the downstream molecular targets of caspases. We established a method for cloning the genes of caspase substrates by two major modifications of the yeast two-hybrid system: (i) both large and small subunits of active caspases were expressed in yeast under ADH1 promoters and the small subunit was fused to the LexA DNA-binding domain; and (ii) a point mutation was introduced that substituted serine for the active site cysteine and thereby prevented proteolytic cleavage of the substrates, possibly stabilizing the enzyme-substrate complexes in yeast. After screening a mouse embryo cDNA expression library by using the bait plasmid for caspase-3, we obtained 13 clones that encoded proteins binding to caspase-3, and showed that 10 clones including gelsolin, an actin-regulatory protein implicated in apoptosis, were cleaved by recombinant caspase-3 in vitro. Using the same bait, we also isolated human gelsolin cDNA from a human thymus cDNA expression library. We showed that human gelsolin was cleaved during Fas-mediated apoptosis in vivo and that the caspase-3 cleavage site of human gelsolin was at D352 of DQTD352G, findings consistent with previous observations on murine gelsolin. In addition, we ascribed the antiapoptotic activity of gelsolin (which we previously reported) to prevention of a step leading to cytochrome c release from the mitochondria into the cytosol. Our results indicate that this cloning method is useful for identification of the substrates of caspases and possibly also of other enzymes.
Suppressing charge noise decoherence in superconducting charge qubits (2008)

We present an experimental realization of the transmon qubit, which is an improved superconducting charge qubit derived from the Cooper pair box. We experimentally verify the predicted exponential suppression of sensitivity to $1∕f$ charge noise. This removes the leading source of dephasing in charge qubits which results in homogeneously broadened transitions with relaxation and dephasing times in the microsecond range. Our systematic characterization of the qubit spectrum, anharmonicity, and charge dispersion shows excellent agreement with theory.
A 32 kbit/s PCM to ADPCM converter (2005)

The structure and characteristics of a PCM to ADPCM converter are described. The main feature of the system is a prediction filter implemented with five cascaded recursive and adaptive second order sections. The filter coefficients are adaptively adjusted according to a gradient algorithm; the four bit adaptive quantizer allows a greater and extensible dynamic range in the converter. Stability is a major problem in adaptive filter design and it is solved here in a very simple manner. In spite of its low complexity the algorithm used yields good results with the different kinds of signals usually found in the telephone network, such as speech and voiceband data. It has been implemented in a 60 channel PCM-ADPCM converter, a small volume and flexible equipment which is going to be introduced in various places in digital telecommunication networks.
Identification of genes involved in DNA replication of the Autographa californica baculovirus. (1994)

By use of a transient replication assay, nine genes involved in DNA replication were identified in the genome of the Autographa californica baculovirus. Six genes encoding helicase, DNA polymerase, IE-1, LEF-1, LEF-2, and LEF-3 are essential for DNA replication while three genes encoding P35, IE-2, and PE38 stimulate DNA replication. No stimulation by the AcMNPV pcna gene, encoding a protein with sequence homology to proliferating-cell nuclear antigen, was observed. A pattern of amino acids found in a number of single-stranded-DNA-binding proteins was identified in the carboxyl-terminal region of IE-1.
Electro-acupuncture Stimulation at Acupoints Reduced the Severity of Hypotension During Anesthesia in Patients Undergoing Liver Transplantation (2011)

Patients with end-stage liver diseases who undergo liver transplantation may suffer from hypotension related to the liver disease itself or related to the surgical procedure. Because electro-acupuncture (EA) at the Neiguan (PC-6) and the Jianshi (PC-5) points influences hemodynamics, we hypothesize that electro-acupuncture at the traditionally used acupuncture points will reduce the severity of hypotension in patients who undergo liver transplantation. Forty patients with end-stage liver disease who underwent orthotropic deceased donor liver transplantation were randomized into two groups. The norepinephrine (NE) group received norepinephrine as a vasoconstrictor, and the electro-acupuncture group received EA at the PC-5 and the PC-6 points for treatment of hypotension during anesthesia for the liver transplantation. The patients were monitored, during the three stages of liver transplantation by using hemodynamic parameters. During the three stages of liver transplantation, there were no significant differences in the hemodynamic measurements including the mean arterial pressure, heart rate and central venous pressure between the two groups (p > 0.05). Electro-acupuncture at the acupuncture points reduced the severity and the incidence of hypotension during anesthesia for liver transplantation.
Niraparib (MK-4827), a novel poly(ADP-Ribose) polymerase inhibitor, radiosensitizes human lung and breast cancer cells (2014)

// Kathleen A. Bridges 1 , Carlo Toniatti 2 , Carolyn A. Buser 3 , Huifeng Liu 1 , Thomas A. Buchholz 4 , and Raymond E. Meyn 1 1 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 2 IRBM/Merck Research Laboratories Rome, Italy 3 Merck Sharp &amp; Dohme Corp., Upper Gwynedd, Pennsylvania 4 Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas Correspondence: Raymond E. Meyn, email: // Keywords : Radiation, PARP, MK-4827, DNA damage, niraparib Received : May 5, 2014 Accepted : June 7, 2014 Published : June 9, 2014 Abstract The aim of this study was to assess niraparib (MK-4827), a novel poly(ADP-Ribose) polymerase (PARP) inhibitor, for its ability to radiosensitize human tumor cells. Human tumor cells derived from lung, breast and prostate cancers were tested for radiosensitization by niraparib using clonogenic survival assays. Both p53 wild-type and p53-defective lines were included. The ability of niraparib to alter the repair of radiation-induced DNA double strand breaks (DSBs) was determined using detection of &gamma;-H2AX foci and RAD51 foci. Clonogenic survival analyses indicated that micromolar concentrations of niraparib radiosensitized tumor cell lines derived from lung, breast, and prostate cancers independently of their p53 status but not cell lines derived from normal tissues. Niraparib also sensitized tumor cells to H 2 O 2 and converted H 2 O 2 -induced single strand breaks (SSBs) into DSBs during DNA replication. These results indicate that human tumor cells are significantly radiosensitized by the potent and selective PARP-1 inhibitor, niraparib, in the in vitro setting. The mechanism of this effect appears to involve a conversion of sublethal SSBs into lethal DSBs during DNA replication due to the inhibition of base excision repair by the drug. Taken together, our findings strongly support the clinical evaluation of niraparib in combination with radiation.
A framework for developing mobile, context-aware applications (2004)

The emergence of truly ubiquitous computing, enabled by the availability of mobile, heterogenous devices that supply context information, is currently hampered by the lack of programming support for the design and development of context-aware applications. We have developed a framework which significantly eases the development of mobile, context-aware applications. The framework allows developers to fuse data from disparate sensors, represent application context, and reason efficiently about context, without the need to write complex code. An event based communication paradigm designed specifically for ad-hoc wireless environments is incorporated, which supports loose coupling between sensors, actuators and application components.
Negative Absolute Temperatures (1956)

Ramsey's criteria for systems capable of negative absolute temperatures are justified. This is done by showing that a thermodynamic proof that the temperature must not be negative breaks down for systems satisfying Ramsey's conditions.
Making designer mutants in model organisms (2014)

Recent advances in the targeted modification of complex eukaryotic genomes have unlocked a new era of genome engineering. From the pioneering work using zinc-finger nucleases (ZFNs), to the advent of the versatile and specific TALEN systems, and most recently the highly accessible CRISPR/Cas9 systems, we now possess an unprecedented ability to analyze developmental processes using sophisticated designer genetic tools. In this Review, we summarize the common approaches and applications of these still-evolving tools as they are being used in the most popular model developmental systems. Excitingly, these robust and simple genomic engineering tools also promise to revolutionize developmental studies using less well established experimental organisms.