gebhart/patrepeval huggingface dataset:
Phylogeny of the Main Bacterial 16S rRNA Sequences in Drentse A Grassland Soils (The Netherlands) (1998)

The main bacteria in peaty, acid grassland soils in the Netherlands were investigated by ribosome isolation, temperature gradient gel electrophoresis, hybridization, cloning, and sequencing. Instead of using only 16S rDNA to determine the sequences present, we focused on rRNA to classify and quantify the most active bacteria. After direct ribosome isolation from soil, a partial amplicon of bacterial 16S rRNA was generated by reverse transcription-PCR. The sequence-specific separation by temperature gradient gel electrophoresis yielded soil-specific fingerprints, which were compared to signals from a clone library of genes coding for 16S rRNA. Cloned 16S rDNA sequences matching with intense bands in the fingerprint were sequenced. The relationships of the sequences to those of cultured organisms of known phylogeny were determined. Most of the amplicons originated from organisms closely related to Bacillus species. Such sequences were also detected by direct dot blot hybridization on soil rRNA: a probe specific for Firmicutes with low G+C content counted for about 50% of all bacterial rRNA. The bacterial activity in Drentse A grassland soil could be estimated by direct dot blot hybridization and sequencing of clones; it was found that about 65% of all the bacterial ribosomes originated from Firmicutes. The most active bacteria apparently were Bacillus species, from which about half of the sequences derived. Other sequences similar to those of gram-positive bacteria were only remotely related to known Firmicutes with a high G+C content. Other sequences were related to Proteobacteria, mainly the alpha subclass.
Capacity evaluation of CDMA-AIC: CDMA cellular system with adaptive interference cancellation (2002)

Direct-sequence code-division multiple-access (DS/CDMA) systems have received considerable attention for future personal communication systems, because of their potential for large capacity, wide coverage and high quality services. This paper describes a CDMA cellular system based on adaptive interference cancellation (CDMA-AIC) with a large capacity. In the CDMA-AIC, each base station employs a single-user type adaptive interference canceller (AIC), which consists of a fractionally chip-spaced code-orthogonalizing filter (COF) and a differential detector. The AIC adaptively removes power dominant multiple access interferences (MAIs) in the cellular system, regardless of whether they are intra-cell interferences or inter-cell interferences, without any information about them, such as spreading codes, signal received timings and channel parameters. Evaluation under the multiple cell environment demonstrates that the reverse link capacity of the CDMA-AIC with QPSK modulation is fourfold or more, compared with the capacity of the CDMA without MAI cancellation. Further, the capacity is less sensitive to transmission power control errors than that of the conventional CDMA systems.
Kinetic data for the crosslinking reaction of polycarboxylic acids with cellulose (1997)

Kinetic data (rate constant, Arrhenius activation energy, frequency factor) of the esterification of polycarboxylic acids (butane‐1, 2, 3, 4‐tetracarboxylic acid, citric acid and pyromellitic acid) have been determined by means of isocratic HPLC measuring the portion of polycarboxylic acid that does not react with cellulosic material. The order of activation energy is as follows: citric acid &gt; butane‐1, 2, 3, 4‐tetracarboxylic acid &gt; pyromellitic acid.
Teaching lasers to control molecules (1992)

We simulate a method to teach a laser pulse sequences to excite specified molecular states. We use a learning procedure to direct the production of pulses based on ``fitness'' information provided by a laboratory measurement device. Over a series of pulses the algorithm learns an optimal sequence. The experimental apparatus, which consists of a laser, a sample of molecules and a measurement device, acts as an analog computer that solves Schr\"odinger's equation n/Iexactly, in real time. We simulate an apparatus that learns to excite specified rotational states in a diatomic molecule.
The Development of an Augmented Reality-Based Data Visualization System for Commissioning of Air Handling Units (2007)

ABSTRACT: This paper discusses the development of an Augmented Reality-based data visualization system that supports commissioning HVAC systems during construction, occupancy, and operations phases. Commissioning is a process that generates a significant amount of data. Therefore a Building Commissioning data model has been developed to effectively manage such data and facilitate the computational support for commissioning work. One of the challenges of this model-based approach has been to reduce the inefficiency caused by the disparate and multiple attributes of the Building Commissioning data. In order to meet this challenge, we aim to develop an Augmented Reality-based data visualization interface which can automatically detects a piece of equipment and visualizes all necessary data relevant to the particular equipment for the commissioning procedures. This paper focuses on the functional requirements and system architecture needed to design such an interface.
Heterologous Protection Against Influenza by Injection of DNA Encoding a Viral Protein (1993)

Cytotoxic T lymphocytes (CTLs) specific for conserved viral antigens can respond to different strains of virus, in contrast to antibodies, which are generally strain-specific. The generation of such CTLs in vivo usually requires endogenous expression of the antigen, as occurs in the case of virus infection. To generate a viral antigen for presentation to the immune system without the limitations of direct peptide delivery or viral vectors, plasmid DNA encoding influenza A nucleoprotein was injected into the quadriceps of BALB/c mice. This resulted in the generation of nucleoprotein-specific CTLs and protection from a subsequent challenge with a heterologous strain of influenza A virus, as measured by decreased viral lung titers, inhibition of mass loss, and increased survival.
Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis (2003)

A bioinformatic analysis of the genome sequence of A. ferrooxidans has revealed candidate genes, metabolic process and control mechanisms potentially involved in aspects of sulfur metabolism. Metabolic modeling provides an important preliminary step in understanding the unusual physiology of this extremophile especially given the severe difficulties involved in its genetic manipulation and biochemical analysis.
PILOT STUDY OF INTRAVITREAL INJECTION OF DICLOFENAC FOR TREATMENT OF MACULAR EDEMA OF VARIOUS ETIOLOGIES (2010)

Up to 8 weeks, intravitreal diclofenac treatment of eyes with macular edema of various etiologies yielded prominent improvement in visual acuity but was not associated with a significant decrease in central macular thickness. No toxic effect of intravitreal diclofenac was observed.
Organization of Cortical Activities Related to Movement in Humans (2000)

The extent and function of synchronization of oscillatory elements in the human sensorimotor cortex during movement remains unclear. Here we determine whether synchronization is distributed in both the spatial and frequency domains and whether it changes according to task. Electrocorticographic (ECoG) signals were recorded from presumed nonpathological areas simultaneously with electromyographic (EMG) signals from upper limb muscles during isometric and phasic movement tasks in humans with subdural electrodes in situ for investigation of epilepsy. Functional mapping of the sensorimotor cortex was performed by previous electrical stimulation through the same ECoG electrodes used for recording. Significant coherence between ECoG and EMG was seen at discrete frequencies in the range of 7-100 Hz. There was no predilection for coherence within a given frequency band to be associated with cortical sites that had been functionally defined as producing contralateral arm motor responses on stimulation. However, coherence with muscle in the 7-14 and 15-30 Hz band tended to be associated with ECoG sites that lay close to or within the central sulcus as determined intraoperatively. The spatial pattern and frequency of coherence changed with different tasks, although similarities in the coherence pattern remained for tasks that shared common features. These findings provide support for the hypothesis that that synchronization at specific frequencies links cortical activities into a functional ensemble during voluntary movement.
Isoaspartyl Post-translational Modification Triggers Autoimmune Responses to Self-proteins (1999)

The normal functioning immune system is programmed to attack foreign pathogens and other foreign proteins while maintaining tolerance to self-proteins. The mechanisms by which tolerance is broken in the initiation of autoimmunity are not completely understood. In the present study, mice immunized with the murine cytochrome c peptide 90-104 showed no response by the B or T cell compartments. However, immunization with the isoaspartyl form of this peptide, where the linkage of Asp(93) to Leu(94) occurs through the beta-carboxyl group, resulted in strong B and T cell autoimmune responses. Antibodies elicited by immunization with the isoaspartyl form of self-peptide were cross-reactive in binding to both isoforms of cytochrome c peptide and to native cytochrome c self-protein. In a similar manner, immunization of mice with the isoaspartyl form of a peptide autoantigen of human systemic lupus erythematosus (SLE) resulted in strong B and T cell responses while mice maintained tolerance to the normal aspartyl form of self-antigen. Isoaspartyl linkages within proteins are enhanced in aging and stressed cells and arise under physiological conditions. These post-translationally modified peptides may serve as an early immunologic stimulus in autoimmune disease.
T cell development in TCR- <i>alpha beta</i> transgenic mice. Analysis using V(D)J recombination substrates. (1995)

The major pathway of intrathymic T cell differentiation leads CD4-8- (DN) T lineage-committed precursors to TCR-alpha beta+ CD4+8- or CD4-84+ (SP) T lymphocytes. The expression of functionally rearranged TCR-alpha beta transgenes (Tg-TCR) may influence thymocyte development by affecting the various selection events that control T cell differentiation. To gain insights into these processes, we have produced double transgenic animals carrying V(D)J recombination substrates in addition to the MHC class I (H-2Kb) allospecific KB5C20 Tg-TCR. We have analyzed substrate rearrangements in purified populations of Tg-TCR+ thymocytes in the situation of positive or negative selection. The profile of rearrangements found in SP thymocytes, positively selected for the Tg-TCR, suggests that expression of the KB5C20 Tg-TCR has only a minimal influence on substrate V(D)J recombination in cells differentiating along the major alpha beta T cell developmental pathway. In contrast, Tg-TCR+ DN thymocytes, in both positively and negatively selecting haplotypes, presented a profile that implies premature cessation of substrate rearrangements. This profile was maintained in peripheral Tg-TCR+ DN cells and was distinct from the one found in CD25+, alpha beta+, or gamma delta+ DN cells purified from mice transgenic for the recombination substrates only. These results are discussed with respect to the possible origin and differentiation pathway of Tg-TCR+ DN and SP cells.
Electromagnetic Navigation during Flexible Bronchoscopy (2003)

Real-time electromagnetic positioning technology coupled with previously acquired CT images is an accurate technology added to standard bronchoscopy to assist in reaching peripheral lung lesions and performing biopsies.
Appendix: Acid-Base Concepts (2002)

The earth remains the only inhabited world known so far, but scientists are finding that the universe abounds with the chemistry of life.
Quasi-breath-hold technique using personalized audio-visual biofeedback for respiratory motion management in radiotherapy (2011)

The proposed QBH technique with personalized audio-visual biofeedback was feasible for respiratory motion management. It showed equivalent or less motion uncertainty and shorter treatment time than the conventional free-breathing-based gating technique did. The technique is expected to optimally compromise between patient comfort and treatment efficiency.
Development and Validation of a Deep-Learning Model to Screen for Hyperkalemia From the Electrocardiogram (2019)

In this study, using only 2 ECG leads, a deep-learning model detected hyperkalemia in patients with renal disease with an AUC of 0.853 to 0.883. The application of artificial intelligence to the ECG may enable screening for hyperkalemia. Prospective studies are warranted.
Packaging of intron-containing genes into retrovirus vectors by alphavirus vectors (1998)

Efficient and controllable expression of a transgene usually requires the presence of intron sequences and much efforts have been made to produce retrovirus vectors that can transduce and integrate genes with introns. However, this has proven difficult because the viral RNA is spliced when it is synthesized in the nucleus of a producer cell. We describe a novel approach to avoid this problem. In our system the retroviral RNA is synthesized in the cytoplasm of the cell, not in the nucleus, in a reaction driven by the Semliki Forest virus (SFV) expression system. The approach was tested with a recombinant Moloney murine leukemia virus genome containing the chloramphenicol acetyltransferase (CAT) gene in association with an intron. This was inserted into a SFV transcription plasmid and the corresponding SFV vector RNA was transcribed in vitro. BHK-21 cells were then transfected with this vector RNA together with two additional SFV vectors that encode the Moloney murine leukemia virus packaging proteins. Retrovirus vectors containing intron-CAT sequences were produced at titers up to 1.3 x 10(6) infectious particles per ml during a 5-hr incubation period. The vectors faithfully transduced the intron-containing CAT gene into NIH 3T3 cells, where the intron-CAT RNA was subjected to efficient splicing and used for high level enzyme expression. Thus, the results show that intron containing genes can be efficiently packaged into retrovirus vectors by the SFV expression system.
Fifty Years of Artificial Reverberation (2012)

The first artificial reverberation algorithms were proposed in the early 1960s, and new, improved algorithms are published regularly. These algorithms have been widely used in music production since the 1970s, and now find applications in new fields, such as game audio. This overview article provides a unified review of the various approaches to digital artificial reverberation. The three main categories have been delay networks, convolution-based algorithms, and physical room models. Delay-network and convolution techniques have been competing in popularity in the music technology field, and are often employed to produce a desired perceptual or artistic effect. In applications including virtual reality, predictive acoustic modeling, and computer-aided design of acoustic spaces, accuracy is desired, and physical models have been mainly used, although, due to their computational complexity, they are currently mainly used for simplified geometries or to generate reverberation impulse responses for use with a convolution method. With the increase of computing power, all these approaches will be available in real time. A recent trend in audio technology is the emulation of analog artificial reverberation units, such as spring reverberators, using signal processing algorithms. As a case study we present an improved parametric model for a spring reverberation unit.
Scalable HAIPE Discovery (2006)

This paper presents a scalable concept for the dynamic discovery of High Assurance Internet Protocol Encryption (HAIPE) devices situated across multiple striped network segments. The term striped in this context refers to traversing from a red (or classified) network to a black (or unclassified) network to a red network in a multiple concatenated manner (i.e., red-black-red-black-red ...). There are many reasons why network segmentation using IP encryption may occur: use of a commercial satellite link, traversing from one secure facility to another on an existing base network, operating over a radio frequency network, and so on. Each of these network segments or enclaves need to be secured (in this case, via IP encryption) which causes the segments to exist. The boundary between red and black sides is assumed to be protected via a HAIPE device (or an equivalent of an IPSEC virtual private network gateway). Our design also addresses mobile enclaves (where whole networks may come and go every 15 minutes) and multi-homed enclaves (where multiple entry/exit points exist). Finding how one traverses this striped environment and operate on a global scale (millions of network) are key challenges and the subject of this paper.
Low-crosstalk 4-channel coarse WDM filter using silica-based planar-lightwave-circuit (2003)

We have demonstrated a 20 nm-spacing 4-channel CWDM waveguide filter, which we fabricated by employing the half-band filter design theory and silica-based PLC fabrication technology. The filter has advantages of compactness, low-loss, low-crosstalk, and a wide passband. This filter comprises a total of 16 MZI stages, which is the largest-scale lattice-form filter yet reported. This filter can be redesigned for 8-channel use or for different wavelength channels. This means that our filter can be employed as a group wavelength channel multi/demultiplexing filter for the DWDM systems. We believe that this wide passband filter will be a key device in optical metro/access networks.
Bottleneck discovery in large-scale networks based on the expected value of per-hop delay (2004)

To relieve congestion in a large-scale network, it is crucial to identify the links, which contribute most to the congestion and then take action to relieve it. This paper presents an algorithm for detecting bottlenecks in a congested large-scale packet-switched network. The strongest bottleneck candidate for a congested session is not necessarily the session link with highest percent utilization or the link with the lowest capacity, but rather the session link with the highest expected value of delay - provided that this link's expected value of delay is significantly greater than the average delay for all links in the session. The approach is based on estimating the per-link expected value of delay (transmission plus queuing) and turning this expected value to a per-link weight. Based on this per-link weight and information collected from an end-to-end QoS monitoring mechanism, the algorithm points to the bottleneck hop where congestion likely occurred. To alleviate congestion, the following actions may be taken: redirect traffic, increase the bottleneck link bandwidth (if possible), implement aggressive traffic shaping, and/ or throttle low priority calls/sessions using the congested link.
Improved Antisense Oligonucleotide Design to Suppress Aberrant SMN2 Gene Transcript Processing: Towards a Treatment for Spinal Muscular Atrophy (2013)

Spinal muscular atrophy (SMA) is caused by loss of the Survival Motor Neuron 1 (SMN1) gene, resulting in reduced SMN protein. Humans possess the additional SMN2 gene (or genes) that does produce low level of full length SMN, but cannot adequately compensate for loss of SMN1 due to aberrant splicing. The majority of SMN2 gene transcripts lack exon 7 and the resultant SMNΔ7 mRNA is translated into an unstable and non-functional protein. Splice intervention therapies to promote exon 7 retention and increase amounts of full-length SMN2 transcript offer great potential as a treatment for SMA patients. Several splice silencing motifs in SMN2 have been identified as potential targets for antisense oligonucleotide mediated splice modification. A strong splice silencer is located downstream of exon 7 in SMN2 intron 7. Antisense oligonucleotides targeting this motif promoted SMN2 exon 7 retention in the mature SMN2 transcripts, with increased SMN expression detected in SMA fibroblasts. We report here systematic optimisation of phosphorodiamidate morpholino oligonucleotides (PMO) that promote exon 7 retention to levels that rescued the phenotype in a severe mouse model of SMA after intracerebroventricular delivery. Furthermore, the PMO gives the longest survival reported to date after a single dosing by ICV.
Transient replication of bovine papilloma virus type 1 plasmids: cis and trans requirements. (1986)

A transient assay has been used to study bovine papilloma virus type 1 (BPV-1) replication. We show that BPV-1 early replication occurs faster than cellular DNA synthesis. Initial replication events are dependent on a gene product(s), encoded by the BPV-1 E1 open reading frame. Mutational analysis of the viral upstream regulatory region shows the requirement of two domains in cis for replication. Domain one, located outside of the viral 69% transforming fragment, is an enhancer-like activity and can be replaced by other known viral enhancers. Domain two lies within sequences previously defined as plasmid maintenance sequence 1. The apparent requirement for a proximal enhancer function for replication may explain why certain BPV-1 constructions, when linked to bacterial plasmid sequences, can be maintained extrachromosomally while others cannot.
Kinetic properties of Streptococcus pneumoniae hyaluronate lyase (2001)

Streptococcus pneumoniae hyaluronate lyase is a surface antigen of this bacterial pathogen, which causes significant mortality and morbidity in human populations worldwide. The primary function of this enzyme is the degradation of hyaluronan, a major component of the extracellular matrix of the tissues of practically all vertebrates. The enzyme uses a processive mode of action to degrade hyaluronan to a final product, an unsaturated disaccharide hyaluronan unit. This catalysis proceeds via a five-step proton acceptance and donation mechanism that includes substrate binding, catalysis, release of the disaccharide product, translocation of the remaining hyaluronan substrate, and proton exchange with microenvironment. Based on the analysis of the three-dimensional structure of the native enzyme and its complexes with hexasaccharide substrate and disaccharide product, several residues have been chosen for mutation studies. These mutated residues included the catalytic residues Asn349, His399, Tyr408, and residues responsible for substrate binding and translocation, Arg243 and Asn580. The comparison of the kinetic properties of the wild-type with the mutant enzymes allowed for the characterization of every mutant and the correlation of the kinetic properties of the enzyme with its structure. The comparison of the wild-type hyaluronate lyase with other polysaccharide-degrading enzymes, the hydrolases endonuclease and glucoamylase, shows striking similarity of K(m)s for all of these different enzymes.