gebhart/patrepeval huggingface dataset:
Extending the Shelf-Life of Chicken Broiler Meat (1982)

Microorganisms involved in the spoilage of poultry meat stored at —2, 4, and 15 C were identified. The numbers of spoilage organisms on poultry meat after storage for different time periods at the above temperatures were determined. Attempts were made to extend the shelf-life of poultry meat by treatment with two solutions containing citric acid, potassium sorbate, and modified cornstarch. Solution 1 consisted of 10% citric acid, 6% potassium sorbate, and 34% modified cornstarch in water (pH 3.2). Solution 2 consisted of 20% citric acid, 6% potassium sorbate, and 24% modified cornstarch in water (pH 2.4). Chicken broiler wings were dipped in boiling water for 10 sec, dipped in Solution 1 or 2 for 60 sec, drained for 3 sec, and packaged individually in polyethylene bags. Untreated poultry meat samples (portion of wing consisting of ulna and radius with attached skin and muscle) had a shelf-life of less than 1 day at 15 C, 7 days at 4 C, and 14 days when stored at —2 C. Wings treated with Solution 1 had a shelf-life of 4 days at 15 C and 14 days at 4 C. Wings treated with Solution 2 had a shelf-life of 6 days at 15 C and longer than 28 days when stored at 4 C. Wings treated with Solution 1 remained acceptable for 1 day when stored at 25 C, whereas those dipped in Solution 2 were acceptable after 2 days. Pseudomonads were identified as the major organisms responsible for spoilage of both treated and untreated samples. Throughout the study, samples treated with Solution 2 had lower microbial counts than samples treated with Solution 1. Treatment of thighs with Solution 1 had no adverse effect on the sensory characteristics of barbecued samples. Samples treated in Solution 2 were scored lower but were not undesirable. Barbecuing consisted of oven baking and basting with a spicy tomato base sauce.
Antibody to the 32K Structural Protein of Infectious Bursal Disease Virus Neutralizes Viral Infectivity in vitro and Confers Protection on Young Chickens (1985)

Chicken sera containing IgG antibodies specific for the 32 000 (32K) mol. wt. structural polypeptide of infectious bursal disease (IBD) virus, as assessed by Western blotting, neutralized the in vitro infectivity of tissue culture-adapted IBD virus. When injected into young chickens, the serum passively protected them from challenge with pathogenic IBD virus. Chickens immunized with the 32K structural polypeptide of IBD virus, prepared by electroelution from SDS-PAGE gels, produced antibody detectable by ELISA and the virus neutralization assay, while chickens immunized with the 37K or 41.5K viral polypeptides synthesized antibody detectable by ELISA, but only very low levels of virus-neutralizing antibody. The immunoglobulin fraction of sera obtained from chickens immunized with the 32K polypeptide, but not the 41.5K polypeptide, passively protected chickens from infection with IBD virus. It is concluded that the 32K polypeptide is a major protective immunogen of IBD virus.
Learning from Examples as an Inverse Problem (2005)

Many works related learning from examples to regularization techniques for inverse problems, emphasizing the strong algorithmic and conceptual analogy of certain learning algorithms with regularization algorithms. In particular it is well known that regularization schemes such as Tikhonov regularization can be effectively used in the context of learning and are closely related to algorithms such as support vector machines. Nevertheless the connection with inverse problem was considered only for the discrete (finite sample) problem and the probabilistic aspects of learning from examples were not taken into account. In this paper we provide a natural extension of such analysis to the continuous (population) case and study the interplay between the discrete and continuous problems. From a theoretical point of view, this allows to draw a clear connection between the consistency approach in learning theory and the stability convergence property in ill-posed inverse problems. The main mathematical result of the paper is a new probabilistic bound for the regularized least-squares algorithm. By means of standard results on the approximation term, the consistency of the algorithm easily follows.
Biosimilars: an overview (2011)

Abstract: “Biologics”, considered one of the fastest growing sectors of the pharmaceutical industry, has introduced many new treatments to life-threatening and rare illnesses. The first generation of biopharmaceutical products manufactured using recombinant technologies was launched in the 1980s, and they are now on the way to patent expiration. As a result, research-based and generic pharmaceutical companies alike are pursuing the opportunity to develop “generic” substitutes for original biologics, herein referred to as biosimilars. However, the process of introducing a biosimilar to an innovator product is far more complex than the relatively straightforward process of introducing a generic equivalent to an innovator product based on a new chemical entity. Biologics are produced by cells in culture or whole organisms, which are inherently more variable than chemical synthesis methods. Therefore, unlike generic pharmaceuticals, it is impossible to generate the same or identical copy of an innovator product. In this way, biosimilars are “similar but not the same” or in other words biosimilars are “the twin but not the clone” to the original biologic innovator product. Therefore the field of biosimilars presents several important challenges, including i) verification of the similarity, ii) the interchangeability of biosimilars and innovator products, iii) the possible need for unique naming to differentiate the various biopharmaceutical products, iv) regulatory framework, v) commercial opportunities as well as guidelines to assist manufacturers in product development, vi) intellectual property rights, and vii) public safety. Keywords: biosimilars, biologics, innovator product, pharmacovigilance, regulatory
An Introduction to Nonlinear Chemical Dynamics (1998)

Just a few decades ago, chemical oscillations were thought to be exotic reactions of only theoretical interest. Now known to govern an array of physical and biological processes, including the regulation of the heart, these oscillations are being studied by a diverse group across the sciences. This book is the first introduction to nonlinear chemical dynamics written specifically for chemists. It covers oscillating reactions, chaos, and chemical pattern formation, and includes numerous practical suggestions on reactor design, data analysis, and computer simulations. Assuming only an undergraduate knowledge of chemistry, the book is an ideal starting point for research in the field. The book begins with a brief history of nonlinear chemical dynamics and a review of the basic mathematics and chemistry. The authors then provide an extensive overview of nonlinear dynamics, starting with the flow reactor and moving on to a detailed discussion of chemical oscillators. Throughout the authors emphasize the chemical mechanistic basis for self-organization. The overview is followed by a series of chapters on more advanced topics, including complex oscillations, biological systems, polymers, interactions between fields and waves, and Turing patterns. Underscoring the hands-on nature of the material, the book concludes with a series of classroom-tested demonstrations and experiments appropriate for an undergraduate laboratory.
Progesterone is Neuroprotective After Acute Experimental Spinal Cord Trauma in Rats (1999)

Rats treated with progesterone had a better clinical and histologic outcome compared with the various control groups. These results indicate potential therapeutic properties of progesterone in the management of acute spinal cord injury.
Wide-band optical communication systems: Part II—Frequency-division multiplexing (1970)

Frequency-division multiplexing techniques offer means for circumventing the bandwidth limitations of optical modulators and detector. Practical broad-band long-distance optical communication system of this type appear feasible and some possible embodiments are described. Calculations are made to determine the approximate information capacity and other characteristics of several 4000-mile repeaterad systems.
Gossip-based aggregation in large dynamic networks (2005)

As computer networks increase in size, become more heterogeneous and span greater geographic distances, applications must be designed to cope with the very large scale, poor reliability, and often, with the extreme dynamism of the underlying network. Aggregation is a key functional building block for such applications: it refers to a set of functions that provide components of a distributed system access to global information including network size, average load, average uptime, location and description of hotspots, and so on. Local access to global information is often very useful, if not indispensable for building applications that are robust and adaptive. For example, in an industrial control application, some aggregate value reaching a threshold may trigger the execution of certain actions; a distributed storage system will want to know the total available free space; load-balancing protocols may benefit from knowing the target average load so as to minimize the load they transfer. We propose a gossip-based protocol for computing aggregate values over network components in a fully decentralized fashion. The class of aggregate functions we can compute is very broad and includes many useful special cases such as counting, averages, sums, products, and extremal values. The protocol is suitable for extremely large and highly dynamic systems due to its proactive structure---all nodes receive the aggregate value continuously, thus being able to track any changes in the system. The protocol is also extremely lightweight, making it suitable for many distributed applications including peer-to-peer and grid computing systems. We demonstrate the efficiency and robustness of our gossip-based protocol both theoretically and experimentally under a variety of scenarios including node and communication failures.
LIM Protein KyoT2 Negatively Regulates Transcription by Association with the RBP-J DNA-Binding Protein (1998)

The RBP-J/Su(H) DNA-binding protein plays a key role in transcriptional regulation by targeting Epstein-Barr virus nuclear antigen 2 (EBNA2) and the intracellular portions of Notch receptors to specific promoters. Using the yeast two-hybrid system, we isolated a LIM-only protein, KyoT, which physically interacts with RBP-J. Differential splicing gave rise to two transcripts of the KyoT gene, KyoT1 and KyoT2, that encoded proteins with four and two LIM domains, respectively. With differential splicing resulting in deletion of an exon, KyoT2 lacked two LIM domains from the C terminus and had a frameshift in the last exon, creating the RBP-J-binding region in the C terminus. KyoT1 had a negligible level of interaction with RBP-J. Strong expression of KyoT mRNAs was detected in skeletal muscle and lung, with a predominance of KyoT1 mRNA. When expressed in F9 embryonal carcinoma cells, KyoT1 and KyoT2 were localized in the cytoplasm and the nucleus, respectively. The binding site of KyoT2 on RBP-J overlaps those of EBNA2 and Notchl but is distinct from that of Hairless, the negative regulator of RBP-J-mediated transcription in Drosophila. KyoT2 but not KyoT1 repressed the RBP-J-mediated transcriptional activation by EBNA2 and Notch1 by competing with them for binding to RBP-J and by dislocating RBP-J from DNA. KyoT2 is a novel negative regulatory molecule for RBP-J-mediated transcription in mammalian systems.
Menaquinone composition of mycolic acid‐containing actinomycetes and some sporoactinomycetes (1985)

The menaquinones of 141 actinomycetes representing the genera Caseobacter, Mycobacterium, Nocardia, Rhodococcus and some related taxa lacking mycolic acids were examined by mass spectrometry. The mycolic acid-containing strains were assigned to four groups on the basis of the predominant isoprenologue detected: Rhodococcus coprophilus, R. equi, R. erythropolis, R. globerulus, R. rhodnii, R. rhodochrous and R. ruber contained dihydrogenated menaquinones with eight isoprene units; Nocardia asteroides, N. brasiliensis, N. carnea, N. otitidis-caviarum and N. transvalensis contained tetrahydrogenated menaquinones with eight isoprene units; Caseobacter polymorphus, R. bronchialis, R. rubropertinctus and R. terrae and representatives of twenty-one approved species of Mycobacterium contained dihydrogenated menaquinones with nine isoprene units; a single strain of 'Mycobacterium album', contained unsaturated menaquinones with nine isoprene units. Actinomycetes containing meso-diaminopimelic acid, arabinose and galactose in the wall peptidoglycan but lacking mycolic acids were recovered in two groups: tetrahydrogenated menaquinones with eight isoprene units were the main components from 'Nocardia' autotrophica and Pseudonocardia thermophila whereas Saccharopolyspora hirsuta and Pseudonocardia spp. contained tetrahydrogenated menaquinones with nine isoprene units. Promicromonospora citrea and 'skin coryneforms' with LL-diaminopimelic acid and glycine in the wall peptidoglycan also contained tetrahydrogenated menaquinones with nine isoprene units as the major isoprenologue. In contrast, representatives of the genera Kitasatoa, Microellobosporia, Streptomyces and Streptoverticillium were characterized by the presence of complex mixtures of tetra-, hexa- and octa-hydrogenated menaquinones with nine isoprene units. The menaquinone data correlate well with other developments in actinomycete systematics and confirm earlier suggestions that menaquinone analyses are of value in both the classification and identification of actinomycetes. Indeed, the data suggest that minimal descriptions of wall chemotype IV taxa should ideally include information on menaquinone composition.
Apoptotic Regression of MCF-7 Xenografts in Nude Mice Treated with the Vitamin D3 Analog, EB1089 (1998)

1,25-Dihydroxyvitamin D3[ 1,25-(OH)2D3] and its synthetic analog EB1089 induce characteristic morphological features of apoptosis in MCF-7 cells in vitro that coincide with up-regulation of clusterin and cathepsin B, proteins associated with apoptosis in the mammary gland, and with down-regulation of Bcl-2, an antiapoptotic protein. To determine whether vitamin D3 compounds could mediate apoptosis of breast tumors in vivo, we treated nude mice carrying established MCF-7 xenografts with the low calcemic vitamin D3 analog EB1089 via daily injection or sustained release pellets for up to 5 weeks. The volume of tumors from mice treated with 45 pmol/day EB1089 was 4-fold lower than that of tumors from vehicle-treated control mice after 5 weeks. The reduced growth of tumors from EB1089-treated mice was associated with characteristic apoptotic morphology and a marked reduction in the proportion of epithelial cells to stroma. After 5 weeks of treatment with EB1089, MCF-7 tumors exhibited a 6-fold increase in DNA fragmentation (as measured by in situ end labeling) relative to that in control tumors. The enhanced rate of apoptosis in tumors from EB1089-treated mice was coupled to a 2-fold reduction in proliferation (as measured by expression of proliferating cell nuclear antigen) compared with that in tumors from control mice. The antitumor effects of EB1089 were evident at doses that had minimal effects on serum calcium and body weight. EB1089 treatment did not alter the growth of xenografts derived from a vitamin D3-resistant variant of MCF-7 cells (MCF-7D3Res cells), which display resistance to EB1089 in vitro, indicating that resistance to EB1089 is maintained in vivo. Tumors derived from both MCF-7 and MCF-7D3Res cells underwent apoptotic regression upon estradiol withdrawal, indicating comparable estrogen dependence of tumors with differential sensitivity to vitamin D3 compounds. These are the first studies to demonstrate apoptotic morphology and regression of human breast tumors in response to treatment with a vitamin D3 analog in vivo and support the concept that vitamin D3 compounds can effectively target human breast cancer.
"Loser Pays" Loses Again (1996)

The most recent congressional attempts to mandate "loser pays" rules for attorneys' fees in many federal civil cases have lost out--at least for the time being--but the push for such legislation has prompted the ABA to adopt a "loser pays" proposal of its own.
Public T Cell Receptor β-Chains Are Not Advantaged during Positive Selection (2008)

Studies of human and murine T cells have shown that public TCR beta-chain rearrangements can dominate the Ag-specific and naive repertoires of distinct individuals. We show that mouse T cells responding to the minor histocompatibility Ag HYDbSmcy share an invariant Vbeta8.2-Jbeta2.3 TCR gene rearrangement. The dominance of this rearrangement shows that it successfully negotiated thymic selection and was highly favored during clonal expansion in all animals examined. We hypothesized that such beta-chains are advantaged during thymic and/or peripheral selection and, as a result, may be over-represented in the naive repertoire. A sequencing study was undertaken to examine the diversity of Vbeta8.2-Jbeta2.3 CDR3 loops from naive T cell repertoires of multiple mice. Public TCR beta-chain sequences were identified across different repertoires and MHC haplotypes. To determine whether such public beta-chains are advantaged during thymic selection, individual chains were followed through T cell development in a series of novel bone marrow competition chimeras. We demonstrate that beta-chains were positively selected with similar efficiency regardless of CDR3 loop sequence. Therefore, the establishment and maintenance of public beta-chains in the periphery is predominantly controlled by post-thymic events through modification of the primary, thymus-derived TCR repertoire.
Fully dispersion-compensated ?500?fs pulse transmission over 50?km single-mode fiber (2005)

We demonstrate essentially distortionless 50 km fiber transmission for approximately 500 fs pulses, using dispersion-compensating fiber and a programmable pulse shaper as a spectral phase equalizer. This distance is approximately five times longer than previously achieved at similar pulse widths.
Highly Efficient CuI-Catalyzed Coupling of Aryl Bromides with Oxazolidinones Using Buchwald's Protocol:  A Short Route to Linezolid and Toloxatone (2003)

[reaction: see text] Coupling of a variety of substituted aryl bromides with oxazolidinones has been achieved using the Buchwald protocol for the amidation of aryl halides. This procedure is exemplified by the synthesis of two medicinally important molecules, linezolid and toloxatone.
Density-based clustering using graphics processors (2009)

During the last few years, GPUs have evolved from simple devices for the display signal preparation into powerful coprocessors that do not only support typical computer graphics tasks but can also be used for general numeric and symbolic computation tasks. As major advantage GPUs provide extremely high parallelism combined with a high bandwidth in memory transfer at low cost. We want to exploit these dvantages in density-based clustering, an important paradigm in clustering since typical algorithms of this category are noise and outlier robust and search for clusters of an arbitrary shape in metric and vector spaces. Moreover, with a time complexity ranging from O(n log n) to O(n2) these algorithms are scalable to large data sets in a database system. In this paper, we propose CUDA-DClust, a massively parallel algorithm for density-based clustering for the use of a Graphics Processing Unit (GPU). While the result of this algorithm is guaranteed to be equivalent to that of DBSCAN, we demonstrate a high speed-up, particularly in combination with a novel index structure for use in GPUs.
Characterization of pyrolysin, a hyperthermoactive serine protease from the archaebacterium Pyrococcus furiosus (1990)

From the hyperthermophilic archaebacterium Pyrococcus furiosus an oxygen-stable, extremely thermostable protease activity, which we designate pyrolysin, has been identified and characterized. Pyrolysin is a cell-envelope associated protease activity high thermo-activity and stability. The temperature optimum is 115°C and half-life values in the absence of substrate are: at least 96 h at 80°C, 9 h at 95°C, 4h at 100°C, 20 min at 105°C and 3 min at 110°C. Pyrolysin is active at a broad pH range between 6.5 and 10.5, and was classified as a serine-type protease activity. Zymogram staining showed the presence of multiple protease bands of about 140, 130, 115, 100 and 65 kDa.
A Template-based Approach to Support Utilization of Clinical Practice Guidelines Within an Electronic Health Record (1998)

Practice guidelines are an integral part of evidence-based health care delivery. When the authors decided to install the clinical documentation component of an electronic health record in a nurse practitioner faculty practice, however, they found that they lacked the resources to integrate it immediately with other systems and components that would support the processing of clinical rules. They were thus challenged to devise an initial approach for decision support related to clinical practice guidelines that did not include interfacing with an inference engine and set of decision rules. The authors developed a prototypic application within the WAVE electronic health record that demonstrates the feasibility of representing a guideline as structured encoded text organized into an online patient-encounter template. Although this approach may be more broadly applicable, it is described within the context of the management of diabetes mellitus by nurse practitioners. The advantages of the approach relate primarily to the integration of the guideline recommendations with the encounter form, the online interaction of the clinician with the system, and the ease of creation and modification of the guideline-based encounter form. However, there are several limitations of the current approach as a result of the inability to do inference and the lack of integration with patient-specific data to trigger specific rules.
Legionnaires' Disease (1993)

Journal Article Legionnaires' Disease Get access Paul H. Edelstein Paul H. Edelstein From the Department of Pathology and Laboratory Medicine and the Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania Correspondence or reprints: Dr. Paul H. Edelstein, Clinical Microbiology Laboratory, Gates Building, 4th Floor, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, 3400 Spruce Street, Philadelphia, Pennsylvania 19104-4283. Search for other works by this author on: Oxford Academic PubMed Google Scholar Clinical Infectious Diseases, Volume 16, Issue 6, June 1993, Pages 741–749, https://doi.org/10.1093/clind/16.6.741 Published: 01 June 1993 Article history Received: 12 February 1993 Published: 01 June 1993