gebhart/patrepeval huggingface dataset:
Efficient Browsing of Web Search Results on Mobile Devices Based on Block Importance Model (2005)

It is expected that more and more people would search the Web when they are on the move. Though conventional search engines can be directly visited from mobile devices with Web browsing capabilities, the information is not as conveniently accessible from a handheld device as it is from desktops. Existing information discovery mechanisms for searching the Web are not well-suited to mobile devices. In this paper, a block importance model is employed to assign importance values to different segments of a Web page, in order to extract and present more condensed search results to mobile users. Based on the block importance model, three presentations for displaying the result pages in different levels of detail have been designed to reduce both the number of user interactions and the overall search time. A set of user study experiments have been carried out to compare the three presentations and a commercial service on typical mobile devices. Experimental results show that our approaches can help users to explore Web search results more efficiently.
Quasi-phase-matched second harmonic generation: tuning and tolerances (1992)

The theory of quasi-phase-matched second-harmonic generation is presented in both the space domain and the wave vector mismatch domain. Departures from ideal quasi-phase matching in periodicity, wavelength, angle of propagation, and temperature are examined to determine the tuning properties and acceptance bandwidths for second-harmonic generation in periodic structures. Numerical examples are tabulated for periodically poled lithium niobate. Various types of errors in the periodicity of these structures are then analyzed to find their effects on the conversion efficiency and on the shape of the tuning curve. This analysis is useful for establishing fabrication tolerances for practical quasi-phase-matched devices. A method of designing structures having desired phase-matching tuning curve shapes is also described. The method makes use of varying domain lengths to establish a varying effective nonlinear coefficient along the interaction length.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Two distinct forms of peptidylprolyl-cis-trans-isomerase are expressed separately in periplasmic and cytoplasmic compartments of Escherichia coli cells (1991)

Peptidylprolyl-cis-trans-isomerase (PPIase) is thought to be essential for protein folding in the cell. Two forms, a and b, of PPIase and their corresponding genes were isolated from Escherichia coli cells. Despite their insensitivity to cyclosporin A (CsA), both amino acid sequences were homologous and related to that of pig cyclophilin, a protein that has PPIase activity sensitive to CsA (Takahashi et al., 1989). PPIase a is found to be identical with the E. coli ORF 190 gene product that was sequenced by Kawamukai et al. (1989) and overexpressed by Liu and Walsh (1990). It is translocated into E. coli periplasmic space with the signal sequence. PPIase b lacks a hydrophobic amino acid stretch which could serve as a signal sequence or a transmembrane domain, and it is detected mainly in the bacterial cytoplasm. These findings indicate that proteins with the ability to assist folding of various polypeptides are located on both sides of the inner membrane. Thus, we propose that the folding of some exported proteins may be catalyzed by the periplasmic proline isomerase and, in turn, that some proteins which have isomerized may not be translocated efficiently.
Molecular cloning and characterization of mitogen-activated protein kinase 2 inToxoplasma gondii (2011)

Mitogen-activated protein kinase (MAPK) pathways are major signal transduction systems by which eukaryotic cells convert environmental cues to intracellular events, such as cell proliferation and differentiation. Toxoplasma gondii is an obligate intracellular protozoan that is both a human and animal pathogen. This Apicomplexan causes significant morbidity and mortality in immune-competent and immune-compromised hosts. In humans, the most common manifestations of T. gondii infections are chorioretinitis in congenital infection and encephalitis in immune-compromised patients, such as patients with advanced AIDS. We have identified a T. gondii homolog of the MAPK family that we have called TgMAPK2. Sequence analyses demonstrated that TgMAPK2 has homology with lower eukaryotic ERK2 but has significant differences from mammalian ERK2. TgMAPK2 has an open reading frame of 2,037 bp, 678 amino acids, and its molecular weight is 73.1 kDa. It contains the typical 12 subdomains of a MAPK and has a TDY motif in the dual phosphorylation and activation subdomains. This suggests that TgMAPK2 may play an important role in stress response. recombinant TgMAPK2 was catalytically active and was not inhibited by a human ERK2 inhibitor, FR180204. A partial TgMAPK2 lacking the ATP-binding motifs GxGxxGxV was successfully regulated by a ligand-controlled destabilization domain (ddFKBP) expression vector system in T. gondii. Since TgMAPK2 is significantly different from its mammalian counterpart, it may be useful as a drug target. This work establishes a foundation for further study for this unique kinase.
Bone morphogenetic proteins: An update on basic biology and clinical relevance (1999)

The regeneration of bone is a remarkable, complex physiological process, and BMPs are a formidable clinical tool to promote its regeneration. By defining roles played by BMPs in developmental biology and bone regeneration, significant progress has been made to identify cell-signaling molecules and their regulators. For example, the regulators of BMPs that include noggin, chordin, cerberus, dan, and gremlin may be harnessed as therapies to offset calcification encountered after total hip arthroplasties. Furthermore, exploiting BMPs and Smads may generate new therapeutic options for bone repair. Another compelling clinical consideration is the trans-acting factor osteoblast-specific factor-2, which can promote osteoblast differentiation. Moreover, the affiliation of osteoblast-specific factor-2 with heritable disorders merits exploration. A recognized daunting challenge includes a carrier/delivery system for the powerful morphogenetic therapeutic tools, as well as osteoprogenitor cells and intracellular transduction and transcriptional factors. In addition, the long-term effects of administering superphysiological doses of rhBMPs to patients must be assessed systematically. A new generation carrier/delivery system may be the answer to offset dosing liabilities as well as to provide residence for exogenous, BMP-receptive osteoprogenitor cells (111,112). The areas highlighted in this review offer fertile territory for thought and research to develop rational clinical treatments to promote bone regeneration and to understand some of the biological roles of BMPs.
Molecular pathobiology of pancreatic adenocarcinoma (1998)

Pancreatic adenocarcinoma is a major cause of cancer death in the United States. Most cases are sporadic and are discovered at late stage when they are not curable by surgery. Information about the molecular biology of pancreatic adenocarcinoma has increased significantly in the last five years with the identification of alterations in the K-ras proto-oncogene and the p16INK4a, p53, FHIT, and DPC4 tumor suppressor genes in a high percentage of tumors. Pancreatic adenocarcinoma is not homogeneous genetically, however, and other genes are clearly involved in some sporadic and heritable tumors. This review summarizes recent data relating to the molecular biology of pancreatic adenocarcinoma with emphasis on features which may be of clinical significance for diagnosis and/or therapy. Molecular genetic alterations that disturb cell cycle regulation in tumor cells can affect their response to chemotherapeutic agents and radiation and many of these genes are targeted in pancreatic adenocarcinoma. Knowledge of these genetic alterations in individual tumors may allow selection of optimal therapeutic strategies for individual patients. Furthermore, molecular detection of oncogene and tumor suppressor gene mutations may find application as screening tests for pancreatic adenocarcinoma at least in high risk populations. Biological therapy aimed at specific oncogenes and tumor suppressor gene replacement therapy protocols for pancreatic adenocarcinoma are beginning and may offer promise in the future.
Peptide Targeting of Tumor Lymph Vessels (2008)

In addition to having a blood vasculature, most normal organs and pathologic conditions involve a second vascular system, the lymphatic vasculature, and many tumors induce the growth of new lymphatic vessels. However, compared to the blood vasculature, very little is known about the lymphatic vessels in tumors. We have used the in vivo phage display technology to map tumor-specific differences in the lymphatic vasculature, and identified peptides that specifically home to tumor lymphatics. Each of these peptides recognizes lymphatic vessels in a different set of tumors, and some of them also recognize tumor cells. Furthermore, these peptides can differentiate lymphatic vasculature of a premalignant lesion from that of a full-blown tumor, indicating tumor stage-specific differences in the lymphatic vessels. None of the lymphatic homing peptides recognizes blood endothelial cells, nor do they home to any normal organ. Of interest, some of our homing peptides are able to penetrate the target cells in a cell type-specific manner. These peptides appear to be able to concentrate in the target tissue, making them particularly efficient delivery vectors for the targeting of therapeutic moieties and imaging agents. Conjugation of the lymphatic homing peptides to drugs provides an opportunity to specifically deliver therapeutic agents into tumors using a route not previously exploited. The surprising degree of selectivity of these lymphatic homing peptides suggests extensive molecular specialization of tumor lymphatic vessels, positing the existence of a molecular lymphatic "zip code" system, as has been previously demonstrated for the tumor blood vasculature.
pH-Dependent Locking of Giant Mesogens in Fibers Drawn from Mussel Byssal Collagens (2008)

Byssal threads are tough collagenous fibers that mussels use to secure themselves against dislodgement by waves in the marine intertidal zone. Here, preCol, a family of hybrid collagens comprising up to 96% of the protein content in certain regions of byssal threads, was purified in mg amounts from mussel foot tissue for the first time. Conditions for drawing preCols into quality fibers ex vivo were investigated. The most important factor affecting fiber formation was the pH of the drawing solution. The morphology and tensile properties of drawn fibers were also characterized and suggest that a liquid crystal mesophase combined with cross-linking by His-metal coordination plays a role in the assembly/mechanics of drawn fibers and likely in native byssal threads as well.
Wireless Daisy Chain and Tree Topology Networks for Smart Cities (2019)

Automation is of prime importance for Smart Cities to optimize resource allocation and usage. For that reason, network designs that allow for efficient and reliable automation are also important. In a fully fledged smart city, billions of devices of varying scale are expected to be connected through private or public networks; these include Smart Connected Street Devices (SCSD) such as traffic signals, devices assisting automated vehicles, board signs for roads and streets, pollution sensors, temperature and humidity sensors, garbage bins, street lights, disaster warning systems etc, and also the appliances a smart home along with the users' personal computing devices. A generic network where the clientele communicates with the server directly may not be feasible in certain applications where the size of the clientele or their physical distance could large, or the unpredictable and erratic bandwidth requirements would pull back efficiency. This work proposes a simple daisy chain network, as well as a tree network using cost-effective wireless communication enabled microcontrollers, to take the transmission load off the server, by relaying commands or requests through the desired network paths. Further, a street- lighting system which cuts the energy consumption by around one order of magnitude is implemented to demonstrate the working.
On the capacity of a cellular CDMA system (1991)

It is shown that, particularly for terrestrial cellular telephony, the interference-suppression feature of CDMA (code division multiple access) can result in a many-fold increase in capacity over analog and even over competing digital techniques. A single-cell system, such as a hubbed satellite network, is addressed, and the basic expression for capacity is developed. The corresponding expressions for a multiple-cell system are derived. and the distribution on the number of users supportable per cell is determined. It is concluded that properly augmented and power-controlled multiple-cell CDMA promises a quantum increase in current cellular capacity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3‐hydroxypropionate cycle (1993)

The phototrophic bacterium Chloroflexus aurantiacus can grow autotrophically but seems not to assimilate CO2 via any of the known autotrophic pathways. Holo [Holo, H. (1989) Arch. Microbiol. 151, 252-256] proposed a new pathway in which 3-hydroxypropionate is formed from acetyl-CoA. Previous studies excluded the operation of known CO2 fixation pathways and provided indirect evidence for the suggested pathway based on 13C-labelling experiments. Here all enzyme activities of the postulated cyclic CO2 fixation mechanism are demonstrated in vitro. In essence, acetyl-CoA is carboxylated and reductively converted via 3-hydroxypropionate to propionyl-CoA. Propionyl-CoA is carboxylated and converted via succinyl-CoA and CoA transfer to malyl-CoA. Malyl-CoA is cleaved to acetyl-CoA and glyoxylate. Thereby, the first CO2 acceptor molecule acetyl-CoA is regenerated, completing the cycle and the net CO2 fixation product glyoxylate is released. This cycle represents the fourth autotrophic pathway in nature and is designated the 3-hydroxypropionate cycle.
Disrupted resting-state brain functional network in methamphetamine abusers: A brain source space study by EEG (2019)

This study aimed to examine the effects of chronic methamphetamine use on the topological organization of whole-brain functional connectivity network (FCN) by reconstruction of neural-activity time series at resting-state. The EEG of 36 individuals with methamphetamine use disorder (IWMUD) and 24 normal controls (NCs) were recorded, pre-processed and source-reconstructed using standardized low-resolution tomography (sLORETA). The brain FCNs of participants were constructed and between-group differences in network topological properties were investigated using graph theoretical analysis. IWMUD showed decreased characteristic path length, increased clustering coefficient and small-world index at delta and gamma frequency bands compared to NCs. Moreover, abnormal changes in inter-regional connectivity and network hubs were observed in all the frequency bands. The results suggest that the IWMUD and NCs have distinct FCNs at all the frequency bands, particularly at the delta and gamma bands, in which deviated small-world brain topology was found in IWMUD.
Trading MIPS and memory for knowledge engineering (1992)

mission to profile and economy of ~e Census Bureau ~dustry and occupation data for individuals in the labor force. For the 1990 Decennial Census, each of an estimated 22 million natural language responses to questions on the census long form had to be classified into one of 232 industry categories and 504 occupation categories. If done fully by hand the cost of this task would be on the order of $15 million.
Three distinct antigens associated with human T-lymphocyte-mediated cytolysis: LFA-1, LFA-2, and LFA-3. (1982)

Monoclonal antibodies were prepared to anti-HLA-DR cytolytic T lymphocytes (CTLs) and screened for inhibition of CTL-mediated killing. Binding of monoclonal antibodies to four types of molecules, LFA-1, LFA-2, LFA-3, and HLA-DR, inhibited killing, suggesting that these molecules participate in the CTL-target cell interaction. The antigens were characterized by immunoprecipitation, crosslinking, NaDodSO4/polyacrylamide gel electrophoresis, and immunofluorescence flow cytometry. The LFA-1 antigen contains alpha and beta polypeptide chains of Mr 177,000 and 95,000 that are noncovalently associated in an alpha 1 beta 1 structure. It is present on both B and T lymphocytes and marks subpopulations that differ in quantitative expression. Human LFA-1 appears to be the homologue of mouse LFA-1. Human LFA-2 is of Mr 49,000 with a minor component of Mr 36,000. It is expressed on CTL lines but not on a B-cell line and in peripheral blood preferentially on T lymphocytes. Human LFA-3 is of Mr 60,000 and is expressed on both B and T lymphocytes.
Voluntary facial expression and hemispheric asymmetry over the frontal cortex (2001)

Brain activity was monitored while 36 participants produced facial configurations denoting anger, disgust, fear, joy, and sadness. EEG alpha power was analyzed during each facial pose, with facial conditions grouped according to the approach/withdrawal motivational model of emotion. This model suggests that "approach" emotions are associated with relatively greater left frontal brain activity whereas "withdrawal" emotions are associated with relatively greater right frontal brain activity. In the context of a bilateral decrease in activation, facial poses of emotions in the withdrawal condition resulted in relatively less left frontal activation in the lateral-frontal, midfrontal and frontal-temporal-central region, but not in the parietal region, as predicted. Findings in the approach condition were less consistently supportive of predictions of the approach/withdrawal model. Implications for the approach/withdrawal model and for the emotion eliciting potential of voluntary facial movement are discussed.
Associations of a Polymorphism in the Ornithine Decarboxylase Gene with Colorectal Cancer Survival (2009)

These results have implications for conditional regulation of polyamine homeostasis and suggest a model in which the ODC1 SNP may be protective for colon adenoma recurrence and detrimental for survival after colon cancer diagnosis.
Investigation of Apoptosis-Related Gene Expression Levels in Preimplantation Biopsies as Predictors of Delayed Kidney Graft Function (2014)

The power to predict DGF of the combination of high BAX/BCL2 expression in PIB and low TLR4 expression in the first day posttransplant peripheral blood observed in the present study is extremely high, in comparison to any other marker or combinations of markers so far published in the literature.
Evaluation of the metal ion requirement of the human deoxyhypusine hydroxylase from HeLa cells using a novel enzyme assay (1996)

Hypusine synthesis in the eukaryotic initiation factor 5A is a unique two-step posttranslational modification. After deoxyhypusine is generated by the deoxyhypusine synthase, the deoxyhypusine hydroxylase (EC 1.14.99.29) catalyzes the formation of mature hypusine. A rapid assay for monitoring the deoxyhypusine hydroxylase activity was established, employing the oxidative cleavage of the hypusyl residue and subsequent extraction of the generated aldehydes. As metal ion chelators have been reported to inhibit the deoxyhypusine hydroxylase, the mechanism of this inhibition and the effect of transition metal ions on enzyme activity were investigated. A ferric ion appears to be essential for enzymatic activity, the inhibition of which is entirely attributed to the metal ion binding capacity of the chelators.
A mutation of ispA that is involved in isoprenoid biogenesis can improve growth of Escherichia coli at low temperatures (2011)

Cells lacking rodZ are defective not only in cell shape, but also in cell growth at low temperatures. Cold-sensitive growth was suppressed by a mutation of ispA without recovery from the round shape, and the mutation improved cell growth of the wild-type at low temperatures.
A Greedy Algorithm for Aligning DNA Sequences (2000)

For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data. An implementation of this algorithm is currently used in a program that assembles the UniGene database at the National Center for Biotechnology Information.
Rapid Detection and Differentiation of Dengue Virus Serotypes by a Real-Time Reverse Transcription-Loop-Mediated Isothermal Amplification Assay (2005)

The development and validation of a one-step, real-time, and quantitative dengue virus serotype-specific reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the 3' noncoding region for the rapid detection and differentiation of dengue virus serotypes are reported. The RT-LAMP assay is very simple and rapid, wherein the amplification can be obtained in 30 min under isothermal conditions at 63 degrees C by employing a set of four serotype-specific primer mixtures through real-time monitoring in an inexpensive turbidimeter. The evaluation of the RT-LAMP assay for use for clinical diagnosis with a limited number of patient serum samples, confirmed to be infected with each serotype, revealed a higher sensitivity by picking up 100% samples as positive, whereas 87% and 81% of the samples were positive by reverse transcription-PCR and virus isolation, respectively. The sensitivity and specificity of the RT-LAMP assay for the detection of viral RNA in patient serum samples with reference to virus isolation were 100% and 93%, respectively. The optimal assay conditions with zero background and no cross-reaction with other closely related members of the Flavivirus family (Japanese encephalitis, West Nile, and St. Louis encephalitis viruses) as well as within the four serotypes of dengue virus were established. None of the serum samples from healthy individuals screened in this study showed any cross-reaction with the four dengue virus serotype-specific RT-LAMP assay primers. These findings demonstrate that RT-LAMP assay has the potential clinical application for detection and differentiation of dengue virus serotypes, especially in developing countries.
Fluorescent probing for RNA molecules by an unnatural base-pair system (2007)

Fluorescent labeling of nucleic acids is widely used in basic research and medical applications. We describe the efficient site-specific incorporation of a fluorescent base analog, 2-amino-6-(2-thienyl)purine (s), into RNA by transcription mediated by an unnatural base pair between s and pyrrole-2-carbaldehyde (Pa). The ribonucleoside 5'-triphosphate of s was site-specifically incorporated into RNA, by T7 RNA polymerase, opposite Pa in DNA templates. The fluorescent intensity of s in RNA molecules changes according to the structural environment. The site-specific s labeling of RNA hairpins and tRNA molecules provided characteristic fluorescent profiles, depending on the labeling sites, temperature and Mg2+ concentration. The Pa-containing DNA templates can be amplified by PCR using 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), another pairing partner of Pa. This site-specific fluorescent probing by the unnatural pair system including the s-Pa and Ds-Pa pairs provides a powerful tool for studying the dynamics of the local structural features of 3D RNA molecules and their intra- and intermolecular interactions.