gebhart/patrepeval huggingface dataset:
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies (2013)

The generation of 260 antibody structures shows that the MAPs database can be used to reliably predict antibody tertiary structures with an average all-atom RMSD of 1.9 Å. Using the broadly neutralizing anti-influenza antibody CH65 and anti-HIV antibody 4E10 as examples, promising starting antibodies for affinity maturation are identified and amino acid changes are traced as antibody affinity maturation occurs.
Preparation of Short Carbon Nanotubes and Application as an Electrode Material in Li‐Ion Batteries (2007)

Abstract A new approach is developed for cutting conventional micrometer‐long entangled carbon nanotubes (CNTs) to short ca. 200 nm long segments with excellent dispersion. CNTs with different lengths are used as anode materials in Li‐ion batteries. The reversible capacity of the Li‐ion batteries is increased and the irreversible capacity is decreased upon shortening the length of the CNTs. The reason for this is that the insertion/extraction of Li ions is easier into/from short CNTs as compared to long CNTs because of the shortened length and the presence of lateral defects. Moreover, short CNTs have a lower electrical resistance and Warburg prefactor, resulting in better rate performance at high current densities. The present study suggests that short segments of CNTs obtained by cutting long CNTs may possess novel properties that may be useful for a wide variety of applications.
BT-Crowds: Crowds-Style Anonymity with Bluetooth and Java (2005)

This paper aims to describe a new idea on how privacy in a Crowds-style network could be enhanced by running it over Bluetooth personal area networking. A potential implementation is described using the Java Bluetooth programming interface. The proposal is called BT-Crowds and it describes a store-and-forward Crowds and remailer-style service which uses the Bluetooth protocol stack and provides a system for privacy-enhanced communications that has some significant benefits over Crowds in fixed networks. It leverages the property of a single Bluetooth user being indistinguishable from a group of many, and the property of ad hoc networks being distributed in physical space.
Hepatitis B and D Virus Infection Among Drug Abusers in Taiwan (1986)

Approximately 15 to 20% of the general population in Taiwan are chronic hepatitis B surface antigen (HBsAg) carriers. However, the incidence of hepatitis D virus (HDV) infection is low (5-8%) in patients with HBsAg-positive chronic liver diseases in this area. To evaluate the prevalence of hepatitis B virus (HBV) and HDV infection among drug abusers in Taiwan, serum samples were collected from 152 drug abusers at the Taipei Municipal Anti-Narcotic Institute and test for HBV and HDV markers. Of these, 24 (15.8%) were HBsAg positive, and only 15 (9.9%) were seronegative for all HBV markers. Of the 115 intravenous drug abusers, serum antibody to hepatitis D antigen (anti-HD) was positive in 78.9% of 19 persons who were HBsAg positive, and in 7.5% of 80 persons who were positive for antibody to HBsAg (anti-HBs). Anti-HD was not detected in the sera from all 37 nonintravenous drug abusers regardless of the status of their HBV markers. Also, none of 63 asymptomatic HBsAg carrier pregnant women or 23 patients with acute type B viral hepatitis had measurable anti-HD in their sera. Thus, the high frequency of HDV detected among Chinese HBsAg carrier intravenous drug abusers in Taiwan is similar to that reported in Western countries.
A portrait of the Semantic Web in action (2001)

Without semantically enriched content, the Web cannot reach its full potential. The authors discuss tools and techniques for generating and processing such content, thus setting a foundation upon which to build the Semantic Web. The authors put a Semantic Web language through its paces and answer questions about how people can use it, such as: how do authors generate semantic descriptions; how do agents discover these descriptions; how can agents integrate information from different sites; and how can users query the Semantic Web.
Past, present and future of hemophilia: a narrative review (2012)

Over the past forty years the availability of coagulation factor replacement therapy has greatly contributed to the improved care of people with hemophilia. Following the blood-borne viral infections in the late 1970s and early 1980, caused by coagulation factor concentrates manufactured using non-virally inactivated pooled plasma, the need for safer treatment became crucial to the hemophilia community. The introduction of virus inactivated plasma-derived coagulation factors and then of recombinant products has revolutionized the care of these people. These therapeutic weapons have improved their quality of life and that of their families and permitted home treatment, i.e., factor replacement therapy at regular intervals in order to prevent both bleeding and the resultant joint damage (i.e. primary prophylaxis). Accordingly, a near normal lifestyle and life-expectancy have been achieved. The main current problem in hemophilia is the onset of alloantibodies inactivating the infused coagulation factor, even though immune tolerance regimens based on long-term daily injections of large dosages of coagulation factors are able to eradicate inhibitors in approximately two-thirds of affected patients. In addition availability of products that bypass the intrinsic coagulation defects have dramatically improved the management of this complication. The major challenges of current treatment regimens, such the short half life of hemophilia therapeutics with need for frequent intravenous injections, encourage the current efforts to produce coagulation factors with more prolonged bioavailability. Finally, intensive research is devoted to gene transfer therapy, the only way to ultimately obtain cure in hemophilia.
Reliability and cost evaluation of third-generation wireless access network topologies: a case study (2002)

The "explosive growth in bursty traffic" changes the network dynamics and requires a good evaluation of various classes of service when designing an access network. From a topological standpoint, the multiservice networks in this paper are heterogeneous systems which integrate both a core and some wireless access networks into an infrastructure similar to third-generation wireless networks. Such networks require reliable and cost-effective solutions to the problem of selecting access technologies for satisfying performance and quality of service requirements related to the services and applications envisioned. This paper analyzes the reliability aspects of some access network topologies to insure a certain level of quality of service at the lowest cost for the end users. It considers a mass market equivalent to 1.6 million subscribers, the objective being to determine the cost the users are ready to pay to benefit from services and applications provided by these multiservice networks. For these purposes, the relative behavior of 3 access-network topologies are studied: the tree with parallel backup links, the ring, and the partially meshed topologies. In ring topology, simulation results show that a great connectivity in the access network is not justified in terms of reliability requirements; the partially meshed topology, even if it has redundant links which affect its cost, outperforms the tree with parallel backup links; and the ring topology is more reliable in terms of disconnected sessions than the tree topology. By considering both reliability and cost, a tree with parallel backup links appears the best topology for the access network and its cost is acceptable for the end user. This study can be extended by: (1) establishing the cost as a function of the quality of service; (2) optimizing the partially meshed topology for more reliable networks; and (3) defining a (shaping) policy to deal with a variety of traffic schemes.
Fitness Components and Ecological Risk of Transgenic Release: A Model Using Japanese Medaka (<i>Oryzias latipes</i>) (2001)

Any release of transgenic organisms into nature is a concern because ecological relationships between genetically engineered organisms and other organisms (including their wild-type conspecifics) are unknown. To address this concern, we developed a method to evaluate risk in which we input estimates of fitness parameters from a founder population into a recurrence model to predict changes in transgene frequency after a simulated transgenic release. With this method, we grouped various aspects of an organism's life cycle into six net fitness components: juvenile viability, adult viability, age at sexual maturity, female fecundity, male fertility, and mating advantage. We estimated these components for wild-type and transgenic individuals using the fish, Japanese medaka (Oryzias latipes). We generalized our model's predictions using various combinations of fitness component values in addition to our experimentally derived estimates. Our model predicted that, for a wide range of parameter values, transgenes could spread in populations despite high juvenile viability costs if transgenes also have sufficiently high positive effects on other fitness components. Sensitivity analyses indicated that transgene effects on age at sexual maturity should have the greatest impact on transgene frequency, followed by juvenile viability, mating advantage, female fecundity, and male fertility, with changes in adult viability, resulting in the least impact.
Motorcycle education and licensing improvement from past research to current demonstration to future implementation (1978)

A comprehensive plan for reducing motorcycle-related deaths, injuries and economic losses is presented. The three-phase plan is concerned with motorcycle operator education/training and licensing improvement. Significant efforts are cited at all levels of government and in the private sector during this decade in the United States. Phase one reports early research and development (1973-1975) creating the Motorcycle Task Analysis and related studies and documentation. The relationship of accident data to task analysis is drawn. Recommendations for improvement in motorcycle accident data reporting systems are given. Phase two describes a current demonstration project (1975-1978) funded by the National Highway Traffic Safety Administration in motorcycle operator licensing improvement. Phase three cites current and anticipated (1978-1982) efforts to implement and evaluate the accident countermeasure potential of a quality motorcycle rider education course. Throughout the paper three themes are evident: 1) the validity and effectiveness of program implementation and change is directly related to antecedent research and development; 2) successful public-private sector traffic safety efforts are rare but possible; and 3) with sufficient long-range planning and institutional commitment, cost effective accident reduction measures can be developed, tested and proven or disproved in actual practice.
Scalable Sweeping-Based Spatial Join (1998)

In this paper, we examine the spatial join problem. In particular, we focus on the case when neither of the inputs is indexed. We present a new algorithm, Scalable Sweep-based Spatial Join (SSSJ), that is based on the distribution-sweeping technique recently proposed in computational geometry, and that is the first to achieve theoretically optimal bounds on internal computation time as well as I/O transfers. We present experimental results based on an efficient implementation of the SSSJ algorithm, and compare it to an improved implementation of the state-of-the-art Partition-Based Spatial-Merge (PBSM) algorithm of Patel and DeWitt. Our SSSJ algorithm performs an initial sorting step along the vertical axis, after which we use the distribution-sweeping technique to partition the input into a number of vertical strips, such that the data in each strip can be efficiently processed by an internal-memory sweepline algorithm. In our experiments, we observed that on real-life two-dimensional...
ON THE NEED FOR DYNAMIC SCHEDULING OF IMAGING SATELLITES (2002)

Imaging satellites are traditionally scheduled in a static fashion; namely the schedule is created off-line and then uploaded to one or more imaging satellites to be executed as an immutable sequence of commands. In this paper, we make the case for dynamic scheduling of imaging satellites. Dynamic schedules will allow satellite systems to take advantage of information gathered during the execution of the schedule and react to changes in the environment, desired tasking, and the availability of resources. We develop the remote sensing scheduling problem and discuss contingency conditions under which the satellite scheduling problem becomes dynamic. We then review existing work on contingency scheduling and conditional scheduling and propose extensions to address the dynamic satellite scheduling problem. Dynamic schedules will yield improved mission schedules and reduced mission costs.
Arterial chemoembolization for hepatocellular carcinoma (1998)

AIM:To study the therapeutic effects of transcatheter arterial three-segment chemoembolization for hepatocellular carcinoma (HCC).METHODS: According to the anatomy of vessels, the tumor capillary networks, muscular arterioles and feeding arteries were successively occluded using lipiodol ultra-fluid (LUF), sinobufagin microsphere (SBMs) and particles of gelatin sponge (PGS). In this series of 80 cases, therapeutic effects were evaluated in 76 cases.RESULTS: There were 22 cases (28.9%) with partial response and 41 (53.9%) with minor response in the 76 evaluated patients. The 6-month, 1-year, 2-year and 3-year survival rates were 97.4%, 86.8%, 46.1% and 27.6% respectively.CONCLUSION: This regimen was a rational chemoembolization method for HCC patients.
Investigation on photoluminescence properties of Eu3+-doped Sr2Mg1-xZnxSi2O7 (0≤x≤1) in UV-VUV region (2009)

Undoped and Eu3+-doped Sr2Mg1-xZnxSi2O7 (0≤x≤1) powder crystal samples were obtained via a conventional solid-state reaction method. The XRD result and FT-IR spectra demonstrated the complete solid-solution as well as lattice distortion between Sr2MgSi2O7 and Sr2ZnSi2O7. The UV emission spectra showed the main emission around 616nm, which implied the non-inversion symmetry around Eu3+ in Sr2Mg1-xZnxSi2O7:Eu3+ (0≤x≤1). The UV excitation spectra exhibited the Eu3+-O2- CT transitions centered at 250nm and 258nm in Sr2MgSi2O7:Eu3+ and Sr2ZnSi2O7:Eu3+, respectively. The emission of Sr2(Mg, Zn)Si2O7:Eu3+ under 147nm light excitation is very weak, which suggests that energy transfer from the host to the activator is not so efficient in Sr2Mg1-xZnxSi2O7:Eu3+ (0≤x≤1) system.
Influence of Working Temperature on Martensitic Transformation in Fe-Cr-Ni Stainless Steel (1970)

In order to investigate the influence of working temperature on the martensitic transformation which is closely related to the mechanical properties, the Fe-Cr-Ni stainless steel sheets containing 16.5∼19%Cr and 7∼11.5%Ni were rolled at several temperatures between room temperature and 200°C, and the saturation flux densities of these specimens were measured to estimate the amount of martensite. Furthermore, the relations among chemical composition, working temperature and amount of generated martensite was considered thermodynamically.The results obtained are summarized as follows. The stainless steel, which has a chemical composition in which the austenite is unstable at nomal temperature, generates more strain-induced martensite with lowering working temperature. In this respect, the rise in working temperature by 10°C is equivalent thermodynamically to the increase in the Ni equivalent by 0.3%. This deduction coincides with experimental results.
Occurrence and distribution of sucrose-metabolizing enzymes in oral streptococci (1976)

Specific growth rates, growth yields, and the level and cellular distribution of three sucrose-metabolizing enzyme activities were determined for seven oral streptococci (Streptococcus mutans strains E49, BHT, 10449, SL-1, and LM-7, S. sanguis 10558, and S. salivarius 25975). Cultures were grown in a fermentor at pH 6 with either 20 mM glucose or 10 mM sucrose. Generation times varied between 21 and 70 min. Whereas some strains grew 10 to 50% more slowly with sucrose than with glucose, others did not. Growth was always logarithmic, and the growth yields were similar. Glcosyl transferase (EC 2.4.1.5) was largely extracellular; in sucrose cultures it was appreciably lower, but no major shift to a cell-associated form was found. In glucose cultures, the activity varied between 4 and 140 IU per 6-liter culture. The glucan formed was mostly or exclusively water insoluble. Glcosyl transferase was stimulated weakly (60% or less) by various dextrans. Fructosyl transferase (EC 2.4.1.10) was primarily extracellular (except in glucose cultures of S. salivarius) and varied between 0 and 337 IU/culture. In S. salivarius, the extracellular fructosyl transferase was induced by sucrose. In all S. Mutans cultures, the total fructosyl transferase activity was lower after growth with sucrose. All strains had extra- and intracellular invertase (EC 3.2.1.26) activity. Total levels varied between 210 and 3,500 IU/culture. Less extracellular activity was present in sucrose cultures. Only S. salivarius had appreciable activity in the cellular particulate fraction. Invertase activity was significantly higher than the combined glucosyl and fructosyl transferase activities in all cultures.
Computing Geographical Scopes of Web Resources (2000)

Many information resources on the web are relevant primarily to limited geographical communities. For instance, web sites containing information on restaurants, theaters, and apartment rentals are relevant primarily to web users in geographical proximity to these locations. In contrast, other information resources are relevant to a broader geographical community. For instance, an on-line newspaper may be relevant to users across the United States. Unfortunately, most current web search engines largely ignore the geographical scope of web resources. In this paper, we introduce techniques for automatically computing the geographical scope of web resources, based on the textual content of the resources, as well as on the geographical distribution of hyperlinks to them. We report an extensive experimental evaluation of our strategies using real web data. Finally, we describe a geographically-aware search engine that we have built using our techniques for determining the geographical scope of web resources.
A Quantitative Approach to Distinguish Pneumonia From Atelectasis Using Computed Tomography Attenuation (2016)

We have established that a threshold HU value can be used to confidently distinguish pneumonia from atelectasis with our standard CT pulmonary angiogram imaging protocol and patient population. This suggests that a similar threshold HU value may be determined for other scanning protocols, and application of this threshold may facilitate a more confident diagnosis of pneumonia and thus speed treatment.
Effects of aging in retinal image quality (1993)

The retinal image quality characterized by the modulation-transfer function of the eye was measured for two groups of subjects aged in the late twenties and mid sixties, respectively. In both groups, we obtained modulation transfer functions by using a double-pass method under the same experimental conditions: 4-mm artificial pupil, paralyzed accommodation, and objective control of the refractive state and centering. Results showed lower values of modulation in the retinal image for older subjects compared with the younger subjects. The modulation transfer function ratio is similar to that previously found for contrast-sensitivity measurements with subjects in the same age groups. These results suggest that a significant fraction of the loss in spatial vision with age has an optical origin. Apart from the well-known increase in intraocular scattering, there also appears to be an increment in ocular aberration that causes an additional reduction in the contrast of retinal images.
The Acetyl Bromide Method Is Faster, Simpler and Presents Best Recovery of Lignin in Different Herbaceous Tissues than Klason and Thioglycolic Acid Methods (2014)

We compared the amount of lignin as determined by the three most traditional methods for lignin measurement in three tissues (sugarcane bagasse, soybean roots and soybean seed coat) contrasting for lignin amount and composition. Although all methods presented high reproducibility, major inconsistencies among them were found. The amount of lignin determined by thioglycolic acid method was severely lower than that provided by the other methods (up to 95%) in all tissues analyzed. Klason method was quite similar to acetyl bromide in tissues containing higher amounts of lignin, but presented lower recovery of lignin in the less lignified tissue. To investigate the causes of the inconsistencies observed, we determined the monomer composition of all plant materials, but found no correlation. We found that the low recovery of lignin presented by the thioglycolic acid method were due losses of lignin in the residues disposed throughout the procedures. The production of furfurals by acetyl bromide method does not explain the differences observed. The acetyl bromide method is the simplest and fastest among the methods evaluated presenting similar or best recovery of lignin in all the tissues assessed.
The UL12.5 Gene Product of Herpes Simplex Virus Type 1 Exhibits Nuclease and Strand Exchange Activities but Does Not Localize to the Nucleus (2004)

The herpes simplex virus type 1 (HSV-1) alkaline nuclease, encoded by the UL12 gene, plays an important role in HSV-1 replication, as a null mutant of UL12 displays a severe growth defect. Although the precise in vivo role of UL12 has not yet been determined, several in vitro activities have been identified for the protein, including endo- and exonuclease activities, interaction with the HSV-1 single-stranded DNA binding protein ICP8, and an ability to promote strand exchange in conjunction with ICP8. In this study, we examined a naturally occurring N-terminally truncated version of UL12 called UL12.5. Previous studies showing that UL12.5 exhibits nuclease activity but is unable to complement a UL12 null virus posed a dilemma and suggested that UL12.5 may lack a critical activity possessed by the full-length protein, UL12. We constructed a recombinant baculovirus capable of expressing UL12.5 and purified soluble UL12.5 from infected insect cells. The purified UL12.5 exhibited both endo- and exonuclease activities but was less active than UL12. Like UL12, UL12.5 could mediate strand exchange with ICP8 and could also be coimmunoprecipitated with ICP8. The primary difference between the two proteins was in their intracellular localization, with UL12 localizing to the nucleus and UL12.5 remaining in the cytoplasm. We mapped a nuclear localization signal to the N terminus of UL12, the domain absent from UL12.5. In addition, when UL12.5 was overexpressed so that some of the enzyme leaked into the nucleus, it was able to partially complement the UL12 null mutant.