gebhart/patrepeval huggingface dataset:
Microbial Diversity of the Brine-Seawater Interface of the Kebrit Deep, Red Sea, Studied via 16S rRNA Gene Sequences and Cultivation Methods (2001)

The brine-seawater interface of the Kebrit Deep, northern Red Sea, was investigated for the presence of microorganisms using phylogenetic analysis combined with cultivation methods. Under strictly anaerobic culture conditions, novel halophiles were isolated. The new rod-shaped isolates belong to the halophilic genus Halanaerobium and are the first representatives of the genus obtained from deep-sea, anaerobic brine pools. Within the genus Halanaerobium, they represent new species which grow chemoorganotrophically at NaCl concentrations ranging from 5 to 34%. The cellular fatty acid compositions are consistent with those of other Halanaerobium representatives, showing unusually large amounts of Delta7 and Delta11 16:1 fatty acids. Phylogenetic analysis of the brine-seawater interface sample revealed the presence of various bacterial 16S rRNA gene sequences dominated by cultivated members of the bacterial domain, with the majority affiliated with the genus Halanaerobium. The new Halanaerobium 16S rRNA clone sequences showed the highest similarity (99.9%) to the sequence of isolate KT-8-13 from the Kebrit Deep brine. In this initial survey, our polyphasic approach demonstrates that novel halophiles thrive in the anaerobic, deep-sea brine pool of the Kebrit Deep, Red Sea. They may contribute significantly to the anaerobic degradation of organic matter enriched at the brine-seawater interface.
Structural basis of a novel heterodimeric Fc for bispecific antibody production (2017)

Bispecific antibodies provide an efficient tool for combinational clinical therapy. Here we have engineered a heterodimeric Fc for bispecific antibodies production by combining the knob-into-hole and electrostatic steering strategies where a bulky hydrophobic residue Phe405 of the IgG CH3 interface is mutated to a charged residue Lys and Lys409 of the corresponding CH3 domain is mutated to Ala. The crystal structure of this Fc heterodimer solved here at 2.7Å resolution revealed how these two mutations resulted a complementary binding interface and explained why F405K mutation could effectively inhibit Fc homodimer formation during protein expression. An anti-HER2 bispecific antibody derived from trastuzumab and pertuzumab was generated by this heterodimeric Fc. It showed comparable or improved efficacy than the combination of trastuzumab and pertuzumab in inhibiting proliferation of cancer cells <i>in vitro</i> and <i>in vivo</i>. Overall this study shows that the heterodimeric Fc engineered here provides an efficient platform for generating active bispecific antibody for cancer treatment.
Further Multiwavelength Observations of the SSA 22 Lyα‐Emitting Blob (2004)

We present new follow-up observations of the sub-mm luminous Ly_alpha-emitting object in the SSA22 z=3.09 galaxy overdensity, referred to as `Blob 1' by Steidel et al.(2000). In particular we discuss high resolution Hubble Space Telescope optical imaging, Owens Valley Radio Observatory spectral imaging, Keck spectroscopy, VLA 20cm radio continuum imaging, and Chandra X-ray observations. We also present a more complete analysis of the existing James Clerk Maxwell Telescope sub-mm data. We detect several optical continuum components which may be associated with the core of the submillimeter emitting region. A radio source at the position of one of the HST components (22:17:25.94, +00:12:38.9) identifies it as the likely counterpart to the submillimeter source. We also tentatively detect the CO(4-3) molecular line, centered on the radio position. We use the CO(4-3) intensity to estimate a limit on the gas mass for the system. The optical morphology of sources within the Ly_alpha cloud appears to be filamentary, while the optical source identified with the radio source has a dense knot which may be an AGN or compact starburst. We obtain a Keck-LRIS spectrum of this object, despite its faintness (R=26.8). The spectrum reveals weak Ly_alpha emission, but no other obvious features, suggesting that the source is not an energetic AGN (or that it is extremely obscured). We use non-detections in deep Chandra X-ray images to constrain the nature of the `Blob'. Although conclusive evidence regarding the nature of the object remains hard to obtain at this redshift, the evidence presented here is at least consistent with a dust-obscured AGN surrounded by a starburst situated at the heart of this giant Ly_alpha cloud.
A blind bandwidth extension method of audio signals based on Volterra series (2012)

In this paper, a blind bandwidth extension method of audio signals is proposed in which the fine structure of high-frequency information is recovered based on Volterra series. Combining with Gaussian mixture model and codebook mapping to adjust the spectrum envelope and energy gain of the extended high-frequency components separately, the bandwidth of audio signals is extended to super-wideband from wideband. Furthermore, the proposed method is applied into a real audio codec. The performance of the proposed method is evaluated through objective and subjective tests on the audio signals selected from MPEG items, and it is found that the proposed method outperforms the chaotic prediction method and nearest-neighbor matching method. When the proposed algorithm is applied into ITU-T G.722.1 wideband audio codec, the performance is comparable with that of G.722.1C super-wideband audio codec at 24 kbps.
Potential Roles for Diatomists in Nanotechnology (2005)

Diatoms produce diverse three-dimensional structures that, due to their exponential rate of growth, may be of use in the manufacture of components for nanotechnology as an alternative to present linear lithographic techniques. Vapor replacement of the silicon permits the conversion of diatom silica valves and other structures to metal/ceramics, with no loss of structure. The literature on diatom nanotechnology is reviewed, along with suggestions on how diatomists might enhance this emerging technology. There is a need for a systematics based catalog of parts (via genomics technologies), improved diatom culture techniques, better understanding of the mechanisms of diatom morphogenesis and motility, and genetic manipulation, mutagenesis, and selection, as via the chemostat-like compustat. Given the self-motility of raphid diatoms, they could form the basis for industrially useful nanobots.
A Novel Tool Using SMA Actuator for cell puncturing (2007)

Biological science are entering micro/nano scale field, micromanipulation tools are indispensable for bringing people from macro scale world to micro scale world. In this paper we developed a novel tool applied for cell puncturing. In this micromanipulation tool, we make use of SMA (Shape Memory Alloy) to drive the manipulator. In order to improve the precision of the system, the output displacement of the tool is controlled by a closed-loop feedback. At the same time, semiconductor refrigeration is applied in the system to reduce the cooling time of SMA. The manipulation strategy is designed and preliminary results are presented. The result showed that the closed-loop is effective in this manipulation system.
Leakage Current in p-Substrate 1.3μm InGaAsP/InP (1985)

Leakage current in p-substrate 1.3 μm InGaAsP/InP Buried Crescent (PBC) lasers has been examinedcompared with n-substrate Buried Crescent (BC) lasers. It has been found that the value of the leakage currentcan be estimated by dV/dI-I (differential resistance vs. current) curve above threshold. The leakage current intypical PBC laser is about one order of magnitude smaller than that in BC laser, in which the leakage currentbecomes a few 10 mA at high temperature (70-80°C) and degrades remarkably the P-I (light output power vs.current) characteristics. In order to achieve excellent characteristics at high temperature and high power levels, it is important to minimize the current flowing into p-blocking layer adjacent to the active region.
A history of non-drug treatment in headache, particularly migraine (2010)

Although new invasive procedures for the treatment of migraine have evolved during the past decades, the application of invasive procedures for this indication is not new. In this review, the history of non-drug treatments for migraine is discussed. Historical texts by physicians known to have written on headache and migraine (hemicrania), well-known books by physicians from the main historical periods up to 1900 and mainstream 20th century neurology handbooks were analysed. A large number of treatments have been tried, based on contemporaneous pathophysiological models that were not only applied to headache, but to medicine in general. Invasive procedures have been used for the more severe types of headache. Many treatments were based on ancient humoral theories up to the early 19th century. A new kind of invasive procedure appeared on the physician's palette in the 19th and 20th century, following the development of new ideas that were based on solid pathophysiology, after the introduction of scientific method into medicine. After its introduction in the mid-18th century, medical electricity became even more popular for the treatment of migraine following the discovery of vasomotor nerves in the mid-19th century, but at the end of that century a more critical attitude appeared. The discovery of the lumbar puncture (1892) and roentgenogram (1895) and increased knowledge of intracranial pressure led to a new series of invasive procedures for therapy-resistant migraine in the early 20th century. Vasospastic theories of migraine led to surgical procedures on the sympathetic nerves. Following the experiments by Graham and Wolff in the 1930s that emphasized the vasodilatation concept of migraine, sympathicolytic procedures again became popular, including vessel ligation of the carotid and middle meningeal arteries. The influence of suggestion and psychological phenomena recognized at the end of the 19th century probably played an important role in many of the procedures applied. These placebo effects, generally more powerful in invasive treatments, are discussed against the background of present-day invasive treatments for headache, where they are still a matter of concern.
Designing intelligent fluids for controlling spray applications (2003)

Recent advances in our understanding of ‘complex fluids’ have lead to the development of new chemical additives in the agricultural industry, which provide more efficient products and a higher level of public and environmental protection. Here we present one example that deals with the improved application of herbicides and pesticides during the spray treatment of plants. Using judiciously chosen dilute polymer solutions, one can simultaneously improve the spray characteristics, droplet deposition, and product retention onto the targeted plant surface. Achieving these combined benefits, requires a delicate balance between fluid hydrodynamics and the molecular interactions that control the phase behaviour of the sprayed solutions.
Segmentation as selective search for object recognition (2011)

For object recognition, the current state-of-the-art is based on exhaustive search. However, to enable the use of more expensive features and classifiers and thereby progress beyond the state-of-the-art, a selective search strategy is needed. Therefore, we adapt segmentation as a selective search by reconsidering segmentation: We propose to generate many approximate locations over few and precise object delineations because (1) an object whose location is never generated can not be recognised and (2) appearance and immediate nearby context are most effective for object recognition. Our method is class-independent and is shown to cover 96.7% of all objects in the Pascal VOC 2007 test set using only 1,536 locations per image. Our selective search enables the use of the more expensive bag-of-words method which we use to substantially improve the state-of-the-art by up to 8.5% for 8 out of 20 classes on the Pascal VOC 2010 detection challenge.
Early apoptosis real-time detection by label-free SERS based on externalized phosphatidylserine (2016)

Apoptosis is a tightly regulated cellular process that plays an essential role in the development, aging, cancer biology, immune response, and pathogenesis of various diseases. Herein, we report a new SERS sensing strategy for in vitro sensitive detection of early apoptotic cells. The principle of this method is to in situ synthesize silver nanoparticles (AgNPs) on the phosphatidylserine (PS) of the apoptotic cell membrane during the early apoptosis, which enables distinguishing normal and apoptotic cells. The total assay time of the presented method is only 10 min, thus being faster, cheaper and simpler than current techniques for the detection of apoptosis. The intrinsic mechanism was verified by different approaches based on externalized phosphatidylserine. In addition, the detection process is real-time and label-free; i.e., the intrinsic SERS spectra from the cellular membrane are directly employed for apoptosis real-time detection, which avoids using additional chemical or biological reagents as external signal indicators. Therefore, our SERS approach may serve as a potentially practical tool for sensitive and real-time detection of early cell apoptosis, complementing the state-of-the-art strategies, e.g. flow cytometry. While further investigation is required to better understand the intrinsic mechanism of the in situ coating method, the current results may provide another choice for real-time detection of early apoptosis.
Chemical Evolution as a Tool for Molecular Discovery (2007)

In modern academic and industrial laboratories, evolutionary strategies are used routinely to identify biopolymers with novel activities. Large libraries of nucleic acids (approximately 10(15)) or peptides and proteins (approximately 10(13)) can be subjected to multiple rounds of selective pressure, amplification, and diversification, yielding individual sequences with desirable properties. Although the evolutionary approach is a powerful search tool, the chemical nature of biopolymers is not suited for all purposes. Application of evolutionary strategies to libraries of arbitrary chemical composition would overcome this problem, and radically change traditional small-molecule discovery. The chemical make-up of in vitro evolution libraries has necessarily been limited, because library synthesis relies on enzymes. A great deal of current research focuses on expanding the chemical repertoire of in vitro evolution by (a) broadening enzyme substrate specificities to include unnatural building blocks, or (b) developing methods to translate DNA sequences into multistep organic syntheses. We discuss the strengths and weaknesses of the approaches, review the successes, and consider the future of chemical evolution as a tool.
Fatal Food-Induced Anaphylaxis (1988)

Fatal food-induced anaphylaxis is rarely reported. In 16 months, we identified seven such cases involving five males and two females, aged 11 to 43 years. All victims were atopic with multiple prior anaphylactic episodes after ingestion of the incriminated food (peanut, four; pecan, one; crab, one; fish, one). In six cases the allergenic food was ingested away from home. Factors contributing to the severity of individual reactions included denial of symptoms, concomitant intake of alcohol, reliance on oral antihistamines alone to treat symptoms, and adrenal suppression by chronic glucocorticoid therapy for coexisting asthma. In no case was epinephrine administered immediately after onset of symptoms. Premortem or postmortem serum samples were available from six victims; in each case elevated levels of IgE antibodies to the incriminated food were demonstrated. Food-sensitive individuals must self-administer epinephrine promptly at the first sign of systemic reaction. Emergency care providers should be aware of cricothyrotomy as a life-saving procedure.
Identifying points of interest by self-tuning clustering (2011)

Deducing trip related information from web-scale datasets has received very large amounts of attention recently. Identifying points of interest (POIs) in geo-tagged photos is one of these problems. The problem can be viewed as a standard clustering problem of partitioning two dimensional objects. In this work, we study spectral clustering which is the first attempt for the POIs identification. However, there is no unified approach to assign the clustering parameters; especially the features of POIs are immensely varying in different metropolitans and locations. To address this, we are intent to study a self-tuning technique which can properly assign the parameters for the clustering needed. Besides geographical information, web photos inherently store rich information. These information are mutually influenced each others and should be taken into trip related mining tasks. To address this, we study reinforcement which constructs the relationship over multiple sources by iterative learning. At last, we thoroughly demonstrate our findings by web scale datasets collected from Flickr.
Computer modeling identifies glucokinase as glucose sensor of pancreatic beta-cells (1984)

Previous work from this laboratory indicates that glucokinase serves as the glucose sensor of pancreatic islets. Here we show by nonlinear computer optimization that the kinetic properties of glucokinase (together with hexokinase, known to be present in islets) account for the observed glycolytic rates in islets as a function of glucose level. Alternative enzymes that have been suggested to perform the same function as glucokinase, N-acetyl-D-glucosamine kinase and glucose-6-phosphatase, are shown to have incompatible properties, including a poor fit, different curve shapes, and unreasonable parameter values resulting from optimization. Their activities in islets are shown to be too low to account for observed glucose usage rates. This work endorses our previous proposal that glucokinase acts as the glucose sensor in pancreatic islet cells.
Experimental Investigation of Modulation Method for Visible-Light Communications (2006)

We have developed a new modulation method - inverted pulse position modulation (I-PPM) and subcarrier inverted pulse position modulation (SC-I-PPM)-that provides superior LED brightness for visible-light communications. In addition, the new modulation method SC-I-PPM is not affected by background light. In this paper, we investigated several modulation methods in details and set up a standard with which to evaluate the performance of modulation methods. Several modulation methods are subjected to experiments to clarify their performance. Experiments show that subcarrier modulation suppresses the influence of background light and that our new modulation best maintains LED brightest.
Chronic Hepatitis B (1990)

Chronic hepatitis B is said to affect at least 5 percent of the world's population and to be the chief cause of cirrhosis and hepatocellular carcinoma.1 The World Health Organization lists hepatitis B as the ninth major cause of death worldwide, close behind chronic pulmonary disease and well ahead of the acquired immunodeficiency syndrome. These estimates suggest that chronic hepatitis B virus (HBV) infection is the most important chronic viral infection affecting humans.The portrayal of chronic hepatitis B as a major health risk must strike most U.S. physicians as somewhat forced or exaggerated. In this country and other developed . . .
On the Intertemporal Risk-Return Relation---a Bayesian Model Comparison Perspective (2004)

The existing empirical studies indicate that inferences on the intertemporal relation between expected return and volatility are highly sensitive to empirical specifications of return dynamics. Glosten, Jagannathan, and Runkle (1993) attempt to resolve this confusing situation by examining several generalizations of the standard GARCH-M model. They conclude a negative risk-return relation solely based on the models that are identified in the first step through a variety of diagnostic tests as relatively “better” models. However, it has not been shown in their study whether the evidence supporting their first-step model selection decision is significant or not. To the extent the strength of sample evidences supporting those selected models is unclear, it remains unconvincing whether their finding of a negative risk-return relation is significant or not. Accordingly, our paper propose a Bayesian model comparison approach to explicitly assess the strength of the evidence in support of the models that typically indicate conflicting signs for the risk-return relation. The empirically computed Bayes factors show that the models that indicate a negative risk-return relation indeed outperform, at a decisive degree, the alternative models that suggest a contrary result. Further, with priors that slightly favor return nonpredictability, evidence still indicates a negative relation after model uncertainty is accounted for. Therefore, our study complements the work of Glosten, Jagannathan, and Runkle (1993) by showing that not only the parameter relating risk to return is estimated to negative and significant for the selected model, but also the selected model is favored by the data at a significant degree. ∗I am grateful to Michael Brandt, Craig MacKinlay, Andrew Metrick, Jessica Wachter, Yihong Xia, and especially my dissertation advisor Robert Stambaugh at the Wharton School of the University of Pennsylvania, for their numerous helpful comments and suggestions. The comments of the seminar participants at the Quantitative Methods in Finance at Sydney and China International Conference in Finance are also appreciated. I am fully responsible for any weakness of the paper. †Correspondence address: LKC School of Business, Singapore Management University, 50 Stamford Road, Singapore 178899. Phone: (65) 6828-0763. Email: lpwang@smu.edu.sg.
Characterization of a family of gamma-ray-induced CHO mutants demonstrates that the ldlA locus is diploid and encodes the low-density lipoprotein receptor. (1986)

The ldlA locus is one of four Chinese hamster ovary (CHO) cell loci which are known to be required for the synthesis of functional low-density lipoprotein (LDL) receptors. Previous studies have suggested that the ldlA locus is diploid and encodes the LDL receptor. To confirm this assignment, we have isolated a partial genomic clone of the Chinese hamster LDL receptor gene and used this and other nucleic acid and antibody probes to study a family of ldlA mutants isolated after gamma-irradiation. Our analysis suggests that there are two LDL receptor alleles in wild-type CHO cells. Each of the three mutants isolated after gamma-irradiation had detectable deletions affecting one of the two LDL receptor alleles. One of the mutants also had a disruption of the remaining allele, resulting in the synthesis of an abnormal receptor precursor which was not subject to Golgi-associated posttranslational glycoprotein processing. The correlation of changes in the expression, structure, and function of LDL receptors with deletions in the LDL receptor genes in these mutants directly demonstrated that the ldlA locus in CHO cells is diploid and encodes the LDL receptor. In addition, our analysis suggests that CHO cells in culture may contain a partial LDL receptor pseudogene.
Studies of the Metabolic Activity of Leukocytes from Patients with a Genetic Abnormality of Phagocytic Function* (1967)

Polymorphonuclear leukocytes from patients with chronic granulomatous disease respond to the phagocytosis of latex particles with normal increments in glucose consumption, lactate production, Krebs' cycle activity, and lipid turnover. The leukocytes of these patients fail to show normal increments in respiration, direct oxidation of glucose, and hydrogen peroxide formation during particle uptake. It appears that the stimulation of respiration with the formation of hydrogen peroxide and stimulation of the direct oxidative pathway of glucose metabolism are closely linked to degranulation and intracellular killing of bacteria by polymorphonuclear leukocytes.