gebhart/patrepeval huggingface dataset:
Identification of Unique Type II Polyketide Synthase Genes in Soil (2005)

Many bacteria, particularly actinomycetes, are known to produce secondary metabolites synthesized by polyketide synthases (PKS). Bacterial polyketides are a particularly rich source of bioactive molecules, many of which are of potential pharmaceutical relevance. To directly access PKS gene diversity from soil, we developed degenerate PCR primers for actinomycete type II KS(alpha) (ketosynthase) genes. Twenty-one soil samples were collected from diverse sources in New Jersey, and their bacterial communities were compared by terminal restriction fragment length polymorphism (TRFLP) analysis of PCR products generated using bacterial 16S rRNA gene primers (27F and 1525R) as well as an actinomycete-specific forward primer. The distribution of actinomycetes was highly variable but correlated with the overall bacterial species composition as determined by TRFLP. Two samples were identified to contain a particularly rich and unique actinomycete community based on their TRFLP patterns. The same samples also contained the greatest diversity of KS(alpha) genes as determined by TRFLP analysis of KS(alpha) PCR products. KS(alpha) PCR products from these and three additional samples with interesting TRFLP pattern were cloned, and seven novel clades of KS(alpha) genes were identified. Greatest sequence diversity was observed in a sample containing a moderate number of peaks in its KS(alpha) TRFLP. The nucleotide sequences were between 74 and 81% identical to known sequences in GenBank. One cluster of sequences was most similar to the KS(alpha) involved in ardacin (glycopeptide antibiotic) production by Kibdelosporangium aridum. The remaining sequences showed greatest similarity to the KS(alpha) genes in pathways producing the angucycline-derived antibiotics simocyclinone, pradimicin, and jasomycin.
Monoclonal Antibodies against Poly(ADP-ribose) Recognize Different Structures of Poly(ADP-ribose) (2020)

The characteristics of two monoclonal antibodies to poly(ADP-Rib) and the various structures of poly(ADP-Rib) recognized by these monoclonal antibodies have been examined. One antibody, IgG monoclonal antibody 10H, reacted with most parts of poly (ADP-Rib) molecules, and its binding was only slightly inhibited by Ado(P)-Rib-P, a monomer unit of the polymer. On hydrolysis of poly(ADP-Rib) protected by the antibody hydrolytic products, such as Ado(P)-Rib-P and Ado(P)-Rib(P)-Rib-P, were almost the same as those from control poly(ADP-Rib). The other antibody, IgM monoclonal antibody 16B, recognized only some parts of poly(ADP-Rib) molecules of larger size, and its binding was not inhibited by Ado(P)-Rib-P. Branched portions were considerably concentrated in parts protected by this antibody. These two monoclonal antibodies are suggested to recognize different structures of poly(ADP-Rib): possibly IgG antibody 10H recognizes linear portions whereas IgM antibody 16B recognizes branched portions of the polymer. These monoclonal antibodies should be useful in studies on the structures, including unknown structures and the locations of these structures in poly(ADP-Rib).
Treatment planning for heavy-ion radiotherapy: calculation and optimization of biologically effective dose (2000)

We describe a novel approach to treatment planning for heavy-ion radiotherapy based on the local effect model (LEM) which allows us to calculate the biologically effective dose not only for the target region but also for the entire irradiation volume. LEM is ideally suited for use as an integral part of treatment planning code systems for active dose shaping devices like the GSI raster scan system. Thus it has been incorporated into our standard treatment planning system for ion therapy (TRiP). Single intensity modulated fields can be optimized with respect to a homogeneous biologically effective dose. The relative biological effectiveness (RBE) is calculated separately for each voxel of the patient CT. Our radiobiologically oriented code system has been used since 1995 for the planning of irradiation experiments with cell cultures and animals such as rats and minipigs. It has been in regular and successful use for patient treatment planning since 1997.
NIMH genetics initiative millennium schizophrenia consortium: Linkage analysis of African-American pedigrees (1998)

The NIMH Genetics Initiative is a multi-site collaborative study designed to create a national resource for genetic studies of complex neuropsychiatric disorders. Schizophrenia pedigrees have been collected at three sites: Washington University, Columbia University, and Harvard University. This article-one in a series that describes the results of a genome-wide scan with 459 short-tandem repeat (STR) markers for susceptibility loci in the NIMH Genetics Initiative schizophrenia sample-presents results for African-American pedigrees. The African-American sample comprises 30 nuclear families and 98 subjects. Seventy-nine of the family members were considered affected by virtue of having received a DSMIII-R diagnosis of schizophrenia (n = 71) or schizoaffective disorder, depressed (n = 8). The families contained a total of 42 independent sib pairs. While no region demonstrated evidence of significant linkage using the criteria suggested by Lander and Kruglyak, several regions, including chromosomes 6q16-6q24, 8pter-8q12, 9q32-9q34, and 15p13-15q12, showed evidence consistent with linkage (P = 0.01-0.05), providing independent support of findings reported in other studies. Moreover, the fact that different genetic loci were identified in this and in the European-American samples, lends credence to the notion that these genetic differences together with differences in environmental exposures may contribute to the reported differences in disease prevalence, severity, comorbidity, and course that has been observed in different racial groups in the United States and elsewhere.
Introduction (1995)

We are about to embark on an exploration, to question the usefulness of computers. Why do we want to do that? After all, computers are already widely used for text processing, for graphics, for administration, for controlling mechanical devices (in cameras, motor cars, aeroplanes and space vehicles…), and for modelling less tangible things (demographic changes, economic forecasts…). So why do we have to question the usefulness of something that is evidently already useful?
Amino Acid Neurotransmitter Candidates: Sodium-Dependent High-Affinity Uptake by Unique Synaptosomal Fractions (1972)

Glutamic and aspartic acids and glycine are accumulated by high-affinity uptake systems into synaptosomal preparations in central nervous tissue. Sodium is required by these high-affinity transports, but not by the low-affinity transports for these and other amino acids. The sodium-requiring amino acid uptake systems label unique synaptosomal fractions. Observations suggest that these amino acids serve specific synaptic functions, presumably as neurotransmitters.
Dual Purkinje-Image Eyetracker (1996)

Abstract : This project presents a new tool to track the eye's angle of rotation. The method employed is that of tracking two reflections, the first and fourth Purkinje-images. Four Purkinje-images are formed within the eye as light is reflected off of cornea and eye lens surfaces. Coincidentally, the first and fourth reflections occur on the same image plane allowing them to be simultaneously captured by a focused charge-coupled device (CCD) camera. Measurements of the relative displacement between these two images reveal the orientation of the eye in space independent of head position in space. An infrared point light source was used to create the Purkinje-images within the eye and a CCD camera was used to capture the images. Computer hardware and software were used to record the eye images and to analyze the image data. Image processing techniques were successfully employed to locate two Purkinje-images within each image of the eye. Through the use of image processing techniques, it is shown that it is feasible to develop a more efficient and lightweight system that is accurate, non-invasive to the subject, and allows the subject to be mobile. Eye tracking systems find application in aids to disabled patients, medical procedures, and military systems. Adapting this work to real-time Eye tracking is a future consideration.
Optimization of using recuperative braking energy on a double-track railway line (2019)

In the introduction, possible ways of reusing energy from recuperation are presented. Next, the paper investigates the possibility of using regenerative braking in the range allowed by the detailed timetable by adopting the method of transferring the recovered electric energy directly to the catenary and immediate use of this energy by another train at the same power section. In the main part of the work, it is shown, that the use of energy recovered from regenerative braking can be optimized by controlling the arrival time of the train to the station within the range allowed by the detailed timetable. The possibilities of using the adopted method are shown on the example of "Tricity" (metropolis of Gdansk, Sopot, Gdynia) suburban railway line no. 250. Finally, selected optimization results are presented and a simplified analysis of the financial benefits resulting from the use and optimization of regenerative braking is presented.
CALACS Operation and Implementation (1999)

This report describes the usage and implementation of CALACS. There are several standalone tasks folded into CALACS, each of which can be run separately or as part of the overall pipeline. Instructions for using them and for the format of the input data are described in this paper. Furthermore, the processing steps for ACS data and the functional flow of the entire pipeline is outlined, along with descriptions of how the memory model was implemented.
C4NP as a High-Volume Manufacturing Method for Fine-Pitch and Lead-Free FlipChip Solder Bumping (2006)

More and more high-end microelectronic devices are being packaged by using solder bumps as the method of interconnection. The two main technologies are flipchip in package (FCiP) and wafer level chip scale package (WLCSP). The main difference is that FCiP devices are placed on a substrate which then interconnects to the PC board (PCB). WLCSP devices connect directly onto the board. There are various solder bumping technologies used in volume production. These include electroplating, solder paste printing, evaporation and the direct attach of preformed solder spheres. FCiP demands many small bumps on tight pitch whereas WLCSP typically requires much larger solder bumps. All these established technologies have important limitations for fine pitch bumping especially when it comes to lead-free solder alloys. The most commonly used method of generating fine-pitch solder bumps is by electroplating the solder. This process is difficult to control and costly, especially when it comes to lead-free solder alloys. These challenges in the transition to lead-free solder bumping has led the European Union to grant exemptions from the ban of lead in certain solder bumping applications. However, the pressure to move to lead-free continues for the entire industry. C4NP (C4-new process) is a new solder bumping technology developed by IBM and commercialized by Suss MicroTec. C4NP addresses the limitations of existing bumping technologies by enabling low-cost, fine pitch bumping using a variety of lead-free solder alloys. C4NP is a solder transfer technology where molten solder is injected into pre-fabricated and reusable glass templates (molds). Mold and wafer are brought into close proximity and solder bumps are transferred onto the entire 300mm (or smaller) wafer in a single process step. C4NP technology is capable of fine pitch bumping while offering the same alloy selection flexibility as solder paste printing. The simplicity of the C4NP process makes it a low cost solution for both, fine-pitch FC in package as well as WLCSP bumping applications. This paper provides a summary of manufacturing and reliability results of C4NP bumped high-end logic devices and how they compare to electroplated lead-free solder bumps. It discusses the relevant process equipment technology and the novel requirements to run a HVM (high volume manufacturing) C4NP process. The paper also talks about the C4NP manufacturing cost model and elaborates on the cost comparison to alternative bumping techniques. The data in this paper is provided by IBM's packaging operation at the Hudson Valley Research Park in East Fishkill, NY
INSTRE (2015)

Over the last several decades, researches on visual object retrieval and recognition have achieved fast and remarkable success. However, while the category-level tasks prevail in the community, the instance-level tasks (especially recognition) have not yet received adequate focuses. Applications such as content-based search engine and robot vision systems have alerted the awareness to bring instance-level tasks into a more realistic and challenging scenario. Motivated by the limited scope of existing instance-level datasets, in this article we propose a new benchmark for INSTance-level visual object REtrieval and REcognition (INSTRE). Compared with existing datasets, INSTRE has the following major properties: (1) balanced data scale, (2) more diverse intraclass instance variations, (3) cluttered and less contextual backgrounds, (4) object localization annotation for each image, (5) well-manipulated double-labelled images for measuring multiple object (within one image) case. We will quantify and visualize the merits of INSTRE data, and extensively compare them against existing datasets. Then on INSTRE, we comprehensively evaluate several popular algorithms to large-scale object retrieval problem with multiple evaluation metrics. Experimental results show that all the methods suffer a performance drop on INSTRE, proving that this field still remains a challenging problem. Finally we integrate these algorithms into a simple yet efficient scheme for recognition and compare it with classification-based methods. Importantly, we introduce the realistic multiobjects recognition problem. All experiments are conducted in both single object case and multiple objects case.
Cross-Coupling Reaction of Alkyl Halides with Grignard Reagents Catalyzed by Ni, Pd, or Cu Complexes with π-Carbon Ligand(s) (2008)

Transition metal-catalyzed cross-coupling reactions of organic halides and pseudo-halides containing a C-X bond (X = I, Br, Cl, OTf, OTs, etc.) with organometallic reagents are among the most important transformations for carbon-carbon bond formation between a variety of sp, sp(2), and sp(3)-hybridized carbon atoms. In particular, researchers have widely employed Ni- and Pd-catalyzed cross-coupling to synthesize complex organic structures from readily available components. The catalytic cycle of this process comprises oxidative addition, transmetalation, and reductive elimination steps. In these reactions, various organometallic reagents could bear a variety of R groups (alkyl, vinyl, aryl, or allyl), but the coupling partner has been primarily limited to sp and sp(2) carbon compounds: alkynes, alkenes, and arenes. With alkyl coupling partners, these reactions typically run into two problems within the catalytic cycle. First, oxidative addition of alkyl halides to a metal catalyst is generally less efficient than that of aryl or alkenyl compounds. Second, the alkylmetal intermediates formed tend to undergo intramolecular beta-hydrogen elimination. In this Account, we describe our efforts to overcome these problems for Ni and Pd chemistry. We have developed new catalytic systems that do not involve M(0) species but proceed via an anionic complex as the key intermediate. For example, we developed a unique cross-coupling reaction of alkyl halides with organomagnesium or organozinc reagents catalyzed by using a 1,3-butadiene as the additive. This reaction follows a new catalytic pathway: the Ni or Pd catalyst reacts first with R-MgX to form an anionic complex, which then reacts with alkyl halides. Bis-dienes were also effective additives for the Ni-catalyzed cross-coupling reaction of organozinc reagents with alkyl halides. This catalytic system tolerates a wide variety of functional groups, including nitriles, ketones, amides, and esters. In addition, we have extended the utility of Cu-catalyzed cross-coupling reactions. With 1-phenylpropyne as an additive, Cu-catalyzed reactions of alkyl chlorides, fluorides, and mesylates with Grignard reagents proceed efficiently. These new catalytic reactions use pi-carbon ligands such as pi-allyl units or alkynes instead of heteroatom ligands such as phosphines or amines. Overall, these reactions provide new methodology for introducing alkyl moieties into organic molecules.
cDNA cloning of FRIL, a lectin from <i>Dolichos lablab</i> , that preserves hematopoietic progenitors in suspension culture (1999)

Ex vivo culture of hematopoietic stem cells is limited by the inability of cytokines to maintain primitive cells without inducing proliferation, differentiation, and subsequent loss of repopulating capacity. We identified recently in extracts of kidney bean and hyacinth bean a mannose-binding lectin, called FRIL, and provide here evidence that this protein appears to satisfy properties of a stem cell preservation factor. FRIL was first identified based on its ability to stimulate NIH 3T3 cells transfected with Flt3, a tyrosine kinase receptor central to regulation of stem cells. Molecular characterization from polypeptide sequencing and identification of the cDNA of hyacinth bean FRIL shows 78% amino acid identity with a mannose-binding lectin of hyacinth beans. Treatment of primitive hematopoietic progenitors in suspension culture with purified hyacinth FRIL alone is able to preserve cells for 1 month without medium changes. In vitro progenitor assays for human hematopoietic cells cultured 3 weeks in FRIL displayed small blast-like colonies that were capable of serial replating and persisted even in the presence of cytokines known to induce differentiation. These results suggest that FRIL is capable of preserving primitive progenitors in suspension culture for prolonged periods. FRIL's clinical utility involving procedures for stem cell transplantation, tumor cell purging before autologous transplantation, and ex vivo cultures used for expansion and stem cell gene therapy currently are being explored.
Structure and Dynamics of Lanthanide(III) Complexes with an <i>N</i>‐Alkylated do3a Ligand (H<sub>3</sub>do3a = 1,4,7,10‐Tetraazacyclododecane‐1,4,7‐triacetic Acid): A Combined Experimental and DFT Study (2010)

Abstract Lanthanide(III) complexes with 10‐benzyl‐1,4,7‐tris(carboxymethyl)‐1,4,7,10‐tetraazacyclododecane (H 3 L ) have been investigated as model compounds of N ‐alkylated Ln III –do3a complexes (H 3 do3a = 1,4,7,10‐tetraazacyclododecane‐1,4,7‐triacetic acid) with potential application in molecular imaging. The X‐ray structures of the [{Ln( L )(H 2 O)} 4 ] · 18H 2 O complexes (Ln = Eu or Tb) show that the metal ion is directly bound to the seven donor atoms of the ligand, with the nine‐coordination sphere completed by an oxygen atom of an inner‐sphere water molecule and an oxygen atom of a carboxylate group from a neighboring [Ln( L )] unit. This results in the formation of tetrameric units through the sharing of carboxylic groups between adjacent [Ln( L )(H 2 O)] complexes. Luminescence lifetime measurements recorded in H 2 O and D 2 O provide a number of coordinated water molecules ( q ) of 1.2, which indicates that the major species that exists in solution contains one inner‐sphere water molecule. The conformational properties of the [Ln( L )(H 2 O)] complexes (Ln = Gd or Lu) have been investigated by using density functional theory (DFT) calculations (B3LYP model). Our results indicate that the Δ(λλλλ) conformation is more stable than the Δ(δδδδ) one for both complexes. The interconversion between these two isomers may proceed either through the inversion of the five‐membered rings formed upon coordination of the 1,4,7,10‐tetraazacyclododecane (cyclen) unit, or through the stepwise rotation of the three acetate pendant arms. According to our calculations, the activation free energy for the arm‐rotation process (5.6 kcal mol –1 ) is much lower than that of the ring‐inversion path (14.6 kcal mol –1 ), which in turn is very similar to those determined experimentally for Ln III (dota) complexes. Thus, a low energy barrier for the arm‐rotation process appears to be responsible for the relatively fast isomer interconversion observed for Ln III ( N ‐alkylated do3a) complexes.
The Macroscopic Kinetics of Rapid Processes of Polymerization in Turbulent Flows (1991)

Abstract The peculiarities of the macrokinetics of rapid polymerization processes in turbulent flows (when the times of the chemical reaction are less than or compatible with those of the reagent mixing) have been discussed. The characteristic specific phenomena have been elucidated, namely: dependence of the molecular characteristics output (MW and MWD) of the polymer formed on the geometry of the reaction volume and on the parameters of the processes of mixing and heat transfer (flow rates, turbulization, boiling, etc.). Such reactions require special methods of investigation and control including those in industries with principally new material-, resource-, and power-saving technology, in particular, for the production of the isobutylene polymers. It is expedient to distinguish the rapid processes of polymerization as a separate class.
Synthesis of Guanidines From Azides: A General and Straightforward Methodology In Carbohydrate Chemistry (2010)

The ability of the guanidinylating reagent N',N''-diBoc-N-triflyl-guanidine (GN-Tf) to react with in situ formed free amines from azides in carbohydrate scaffolds was explored. This reaction proved to be an efficient method to prepare guanidine derivatives in a one-pot manner with good to excellent yields, either with primary or secondary azides with different substitution patterns. Labile protecting groups such as benzyl ethers are not removed under these hydrogenolytic conditions.
A backward-wave antenna based on negative refractive index L-C networks (2003)

Recently, there has been significant interest in materials with simultaneously negative permeability and permittivity, also referred to as negative refractive index metamaterials. Metamaterials comprised of straight metal wires and split ring resonators operating in the long wavelength regime exhibit a microwave frequency range with simultaneously negative values of effective permeability and permittivity. We use a 1D L-C loaded transmission line network supporting fast backward-wave propagation to demonstrate characteristics analogous to "reversed Cherenkov radiation". A novel backward-wave radiating structure inspired by negative refractive index L-C materials is proposed. A CPW-based printed configuration is presented with preliminary method of moments simulation results. The simulated E-plane pattern at 15 GHz shows radiation towards the backfire direction in the far-field pattern, clearly indicating the excitation of a backward wave. Since the transverse dimension of the array is electrically short, the structure is backed by a long metallic trough. The trough acts as a waveguide below cut-off and recovers the back radiation, resulting in unidirectional far-field patterns.
Wavelet-like filter banks: design and some application results (2002)

This paper extends the design approach based on time-domain formulation for perfect reconstruction filter banks to the design of wavelet-like filter banks by numerical optimisation of a set of non-linear simultaneous equations satisfying a number of basic properties desired. Also presented in the paper are their performances on image compression and denoising applications compared with the traditional Daubechies (1988) wavelet filter banks, thereby demonstrating the potential and the effectiveness of the wavelet-like filter banks designed.