gebhart/patrepeval huggingface dataset:
CRISPR/dCas9-based metabolic pathway engineering for the systematic optimization of exopolysaccharide biosynthesis in Streptococcus thermophilus (2022)

Streptococcus thermophilus is used extensively in the dairy industry and has shown great promise as a chassis cell for the biosynthesis of high-value metabolites. However, metabolic engineering in S. thermophilus lacks effective genetic modification tools to modulate gene expression to relieve metabolic burden and maximize the production of desired compounds. Here, we developed a clustered regularly interspaced short palindromic repeats interference (CRISPRi) system for efficient gene transcriptional modulation in S. thermophilus. Our CRISPRi system typically achieved 66 to 98% knockdown of single or multiple gene expression. We used CRISPRi for the biosynthesis of a new exopolysaccharide (EPS) as a paradigm model. Repression of galK at module of uridine diphosphate glucose sugar metabolism and overexpression of epsA and epsE at EPS synthesis module resulted in an approximately 2-fold increase in EPS titer (277 mg/L) when compared with a control strain. This study demonstrated the effectiveness of CRISPRi as a powerful metabolic engineering tool and synthetic biology strategy for S. thermophilus.
Growth of silicone-immobilized bacteria on polycarbonate membrane filters, a technique to study microcolony formation under anaerobic conditions (1997)

A technique was developed to study microcolony formation by silicone-immobilized bacteria on polycarbonate membrane filters under anaerobic conditions. A sudden shift to anaerobiosis was obtained by submerging the filters in medium which was depleted for oxygen by a pure culture of bacteria. The technique was used to demonstrate that preinduction of nitrate reductase under low-oxygen conditions was necessary for nonfermenting, nitrate-respiring bacteria, e.g., Pseudomonas spp., to cope with a sudden lack of oxygen. In contrast, nitrate-respiring, fermenting bacteria, e.g., Bacillus and Escherichia spp., formed microcolonies under anaerobic conditions with or without the presence of nitrate and irrespective of aerobic or anaerobic preculture conditions.
Identification of Guided-Wave Modes in Pipings of Power Plants by using Air-coupled Transducer (2004)

In order to inspect the piping effectively, one of the important components in the facility of power plants, the ultrasonic guided wave was generated by a tomb transducer and was received in a non-contact fashion by using an air-coupled transducer. The guided wave modes that ran be generated by the comb transducer in piping are predicted from the theoretical dispersion curves and the element spacing of a comb transducer. Moreover, to receive the specific modes, the receiving angle of the air-coupled transducer is calculated from Snell's law between the phase velocities of guided waves and the sound velocity of air. The guided wave modes obtained in experiments are identified from the result of time-frequency analysis such as wavelet transform and two-dimensional fast Fourier transform.
A Review of EEG Signal Classifier Based on Deep Learning (2018)

Electroencephalogram (EEG) signal recognition is an active research topic in the field of artificial intelligence and has been gaining extensive attention and engineering communities. This technology is an important basis of human computer interaction and many other fields. The deep learning theory has made remarkable achievements on feature extraction and gradually extended to the time sequences of EEG research. This paper reviews the traditional feature extraction of EEG recognition and discuss the traditional classification methods of EEG recognition such as linear discriminant analysis (LDA), support vector machine (SVM) and long short time memory (LSTM). Finally, this paper summarizes advantages and disadvantages of these methods. Through the feature extraction by the wavelet transform and LSTM classification, it has achieved 98% accuracy and verified that LSTM is suitable for EEG signal with time sequence feature.
Quantitative phase imaging by using a position sensitive detector (2018)

We present a phase imaging system using a novel non-interferometric approach. We overcome the limitations in spatial resolution, optical efficiency, and dynamic range that are found in Shack-Hartmann sensors. To do so, we sample the wavefront using a digital micromirror device. A single lens forms a time-dependent light distribution on its focal plane, where a position detector is placed. Our approach is lenslet-free and does not use any kind of iterative or unwrap algorithm to recover the phase information. The validity of our approach is demonstrated by performing both aberration sensing and phase imaging of transparent samples.
Supplementary Figure Legends 1-3 from Chemotherapy-Induced Genotoxic Stress Promotes Sensitivity to Natural Killer Cell Cytotoxicity by Enabling Missing-Self Recognition (2023)

Supplementary Figure Legends 1-3 from Chemotherapy-Induced Genotoxic Stress Promotes Sensitivity to Natural Killer Cell Cytotoxicity by Enabling Missing-Self Recognition
Multi-Agent Based Autonomic Network Management Architecture (2021)

The advent of network softwarization is enabling multiple innovative solutions through software-defined networking (SDN) and network function virtualization (NFV). Specifically, network softwarization paves the way for autonomic and intelligent networking, which has gained popularity in the research community. Along with the arrival of 5G and beyond, which interconnects billions of devices, the complexity of network management is significantly increasing both investments and operational costs. Autonomic networking is the creation of self-organizing, self-managing, and self-protecting networks, to afford the network management complexes and heterogeneous networks. To achieve full network automation, various aspects of networking need to be addressed. So, this article proposes a novel architecture for the multi-agent-based network automation of the network management system (MANA-NMS). The architecture rely on network function atomization, which defines atomic decision-making units. Such units could represent virtual network functions. These atomic units are autonomous and adaptive. First, the article presents a theoretical discussion of the challenges arisen by automating the decision-making process. Next, the proposed multi-agent system is presented along with its mathematical modeling. Finally, MANA-NMS architecture is mathematically evaluated from functionality, reliability, latency, and resource consumption performance perspectives.
Bridging the gap between technology and business strategy (1995)

Innovation is now recognized as the key to bridging the gap between technology and business strategy. In response to this, a research project was established seeking to examine the current conceptual understanding of innovation, and establish patterns, if any, that might exist in the management practice of innovation across business organizations. Reviews the overall research objectives and methodology. Examines the current conception of innovation. Discusses the design of two questionnaires to facilitate the research, and the results of a pilot study recently carried out involving two different UK companies based in the Midlands.
Lipografting and stromal vascular fractions of adipose tissue in the treatment of patients with radiation-induced rectovaginal fistulas (2019)

Objective: to analyze the efficacy of a newly developed method for the treatment of radiation-induced rectovaginal fistulas using autologous adipose tissue obtained by aspiration liposuction.Materials and methods. This retrospective study included 24 patients with radiation-induced rectovaginal fistulas that arose after chemoradiotherapy for malignant tumors of the female reproductive system. All patients underwent colostomy before treatment initiation. Study participants received 1 to 5 injections (mean number 3) of autologous adipose-derived regenerative cells. The main indication for the procedure was the presence of a fistula, diagnosed at least 6 months after the last course of radiation therapy. We evaluated time to fistula healing, results of elastometry, and presence of complications.Results. The mean total dose received by patients during their radiotherapy was 60 Gy; median time to initiation of fistula treatment was 15 months. Before the injection of adipose-derived regenerative cells, the mean fistula diameter was 2.50 + 0.46 cm, whereas after 3 months, it reduced to 1.35 + 0.47 cm and after 6 months, it was 1.12 + 0.47 cm. All patients had complete epithelialization of the defect. No cases of fistula recurrence were registered.Conclusion. We demonstrated high efficacy of a new reconstructive method for radiation-induced rectovaginal fistulas with autologous adipose tissue obtained by aspiration liposuction. Its effectiveness is confirmed by complete fistula closure and restoration of intestinal continuity in all study participants.
[Endovascular repair of abdominal aortic aneurysms]. (2006)

Abdominal aortic aneurysms (AAA) continue to be a major source of morbidity and mortality. The transfemoral placement of endoluminal stent-grafts for the treatment of AAAs, first described in 1991, offers a minimally invasive technique for the treatment of AAAs. The technology of endovascular repair of AAAs has progressed rapidly and the approach has proven to be safe and effective in the short- to mid-term. The spectrum of patients who are candidates for endovascular repair and the devices available continue to expand. However, endovascular repair of AAAs remains a relatively novel technique, and there is still much to be learned about its long-term durability.
Fault-tolerance and two-level pipelining in VLSI systolic arrays (2018)

Computer Science Department
The proteins encoded by c-akt and v-akt differ in post-translational modification, subcellular localization and oncogenic potential. (1993)

The acute retrovirus AKT8, isolated from an AKR mouse T-cell lymphoma, transforms mink lung cells in culture and is oncogenic when inoculated into newborn mice. The oncogene carried by this virus, v-akt, arose by recombination between Gag and the 5' untranslated region of the cellular gene c-akt. v-akt encodes a 105 kilodalton (kd) Gag-Akt fusion protein which is phosphorylated on serine and threonine residues. c-akt encodes a 55 kd serine-threonine protein-kinase, which is related to members of the protein kinase C (PKC) family and contains an SH2-like domain. The SH2-like and catalytic domains of Akt were expressed in E. coli as fusions to the carboxy-terminus of the Maltose binding protein (MBP). Antibodies against these proteins were raised in rabbits and they were used to determine the potential myristylation and subcellular localization of the v-akt and c-akt protein products. Immunoprecipitation of v-akt and c-akt from lysates of [35S]methionine and [3H]myristic acid labeled AKT8 transformed mink lung cells revealed that only v-akt was myristylated. Fractionation of Dounce-homogenized cellular extracts from uninfected and v-akt-transformed mink lung and PA317 cells and from uninfected PC12 cells by differential centrifugation showed that while the c-akt protein was localized primarily in the cytosol (90%), the v-akt protein was dispersed among the cellular compartments with approximately 40% on the plasma membranes, approximately 30% in the nucleus and approximately 30% in the cytosol. To determine whether the differences in post-translational modification and subcellular distribution between c-akt and v-akt translated into oncogenicity differences between the two proteins, we used retrovirus based constructs to express them both in the nontumorigenic rat T cell lymphoma line 5675. Intraperitoneal (IP) inoculation of the parental and c-akt expressing 5675 cells in nude Balb/c mice revealed that neither was oncogenic. In sharp contrast to these results, v-akt expressing 5675 cells inoculated in nude Balb/c mice were found to be highly oncogenic.
An atypical systemic form of chronic active EBV infection (2020)

The World Health Organization classification of Tumors of Hematopoietic and Lymphoid Tissues recognizes two broad forms of EBV-positive lymphoproliferative disorders of childhood: (1) EBV-positive ...
ZnO‐Nanowire‐Inserted GaN/ZnO Heterojunction Light‐Emitting Diodes (2007)

Out of the blue: Light-emitting diodes were obtained by fabricating p+-GaN film/n-ZnO nanowire array/n+-ZnO film structures (see figure). Blue electroluminescence (EL) emission was observed from the nanowire-inserted heterojunction diodes under forward bias. These diodes exhibited improved EL emission and injection current compared to those of film-based heterojunction diodes.
Extreme statistics in Raman fiber amplifiers : influence of pump depletion and dispersion (2010)

OSA 2010 NonLinear Photonics Best Student Poster Award
Multifunctional oil well logging (2005)

In this paper, the principle and circuit design of the multifunctional logging tool is introduced. The modular circuit can function as several kinds of current logging tools by executing the corresponding instructions.
Manipulation of an axisymmetric jet using continuous control jets (2006)

The mechanisms associated with the interaction of an axisymmetric free jet (d e = 4 mm; Re U e = 26 500 and 6600) with two continuous control jets on mixing, spreading and direction were examined experimentally. The flow field was visualized and measured using particle image velocimetry, where the interaction of the main jet with the control jets was investigated for different momentum coefficients, streamwise interaction locations and Reynolds numbers. Applying control at low momentum coefficients results in a stabilizing effect, where near the orifice the main jet is stretched such that the turbulent quantities are decreased. However, when control is applied at high momentum coefficients, enhanced mixing and destabilization is obtained, as well as an earlier transition to turbulence and an alteration of the large coherent structures of the main jet. Moreover, the effectiveness of the control jets in altering the main jet flow is more pronounced when the interaction occurs closer to the main jet exit as well as at lower Reynolds numbers.
Stereospecificity and Self-Selectivity in the Generation of a Chiral Molecular Tetrahedron by Metal-Assisted Self-Assembly (1998)

The chiral bidentate ligand (S,S)-1 reacts stereospecifically with Ga<sup>3+</sup> to generate a [Ga<sub>4</sub> (L)<sub>6</sub> ]<sup>12-</sup> molecular tetrahedron although similar ligands generate [Ga<sub>2</sub> (L)<sub>3</sub> ]<sup>6-</sup> complexes. The assembly of this complex is self-selective as a racemic mixture of the ligand sorts by chirality to generate an enantiomeric pair of homochiral complexes.
Integrating Co-design Practices into the Development of Mobile Science Collaboratories (2009)

Scientific practices increasingly incorporate sensors for data capture, information visualization for data analysis, and low-cost mobile devices for field-based inquiries incorporating open Web standards. While a broad range of design approaches for developing technology-enhanced learning has been used by researchers and practitioners for the last 15 years, significant challenges for educational use remain as new technologies and user experiences continually evolve outside the classroom. We focus on the specific design challenge of how to initiate the co-design process together with teachers, researchers, scientists, designers, and developers in order to devise and develop mobile science collaboratories that support open inquiry-based learning in ecology education. The outcomes presented in this paper point towards the need for additional methods to support co-design that take into consideration future user experiences needed for developing and implementing these types of learning activities.
Granulysin-dependent killing of intracellular and extracellular Mycobacterium tuberculosis by V gamma 9/V delta 2 T lymphocytes (2001)

Contribution of V gamma9/V delta2 T lymphocytes to immune protection against Mycobacterium tuberculosis is still a matter of debate. It was reported earlier that V gamma9/V delta2 T lymphocytes kill macrophages harboring live M. tuberculosis through a granule-dependent mechanism that results in killing of intracellular bacilli. This study found that V gamma9/V delta2 T lymphocytes reduce the viability of both extracellular and intracellular M. tuberculosis. Granulysin and perforin, both detected in V gamma9/V delta2 T lymphocytes, play a major role, which indicates that V gamma9/V deltaT lymphocytes directly contribute to a protective host response against M. tuberculosis infection.
The effect of clock and carrier phase drifts on the performance of a direct sequence spread spectrum multiple-access system (2003)

A direct-sequence spread-spectrum multiple-access network is discussed. The probability of symbol error in such a network is dependent on the carrier and spreading code chip phases of the interfering terminals with respect to the signal of interest. As a result, for a given total interference power the performance is worse for the case of one strong interferer when compared to the case of many weak interferers where the Gaussian assumption on the multiple-access interference holds. It is shown that if there is an offset between the carrier and spreading code frequencies of the signals, then the difference in performance between the cases of a set of balanced and a set of unbalanced interferers is drastically reduced.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Defining principles that influence antimicrobial peptide activity against capsulated Klebsiella pneumoniae (2020)

The extracellular polysaccharide capsule of <i>Klebsiella pneumoniae</i> resists penetration by antimicrobials and protects the bacteria from the innate immune system. Host antimicrobial peptides are inactivated by the capsule as it impedes their penetration to the bacterial membrane. While the capsule sequesters most peptides, a few antimicrobial peptides have been identified that retain activity against encapsulated <i>K. pneumoniae,</i> suggesting that this bacterial defense can be overcome. However, it is unclear what factors allow peptides to avoid capsule inhibition. To address this, we created a peptide analog with strong antimicrobial activity toward several <i>K. pneumoniae</i> strains from a previously inactive peptide. We characterized the effects of these two peptides on <i>K. pneumoniae</i>, along with their physical interactions with <i>K. pneumoniae</i> capsule. Both peptides disrupted bacterial cell membranes, but only the active peptide displayed this activity against capsulated <i>K. pneumoniae</i> Unexpectedly, the active peptide showed no decrease in capsule binding, but did lose secondary structure in a capsule-dependent fashion compared with the inactive parent peptide. We found that these characteristics are associated with capsule-peptide aggregation, leading to disruption of the <i>K. pneumoniae</i> capsule. Our findings reveal a potential mechanism for disrupting the protective barrier that <i>K. pneumoniae</i> uses to avoid the immune system and last-resort antibiotics.
Mutation of cysteine 214 in Gi1 alpha subunit abolishes its endogenous GTPase activity (2004)

The functional consequences of the mutation of a conserved Cys-214 in Galpha(i1) have been investigated. We reported herein that substitutions of Cys-214 of Galpha(i1) to either alanine or tryptophan abolished the intrinsic GTPase activity. Free phosphate release from [32P]GTP-bound Galpha(i1) C214A or [32P]GTP-bound Galpha(i1) C214W was at least 30-fold lower than that of the wild-type Galpha(i1) in single-turnover GTPase assays. Consistently, tryptic proteolysis of C214A and C214W proteins showed that they were partially protected by GTP, further confirming that the GTPase activity in both mutant proteins was impaired. Expression of C214A or C214W mutants in Chinese hamster ovary K1 cells caused significant inhibition of forskolin-stimulated adenylate cyclase activity. However, the mutations did not significantly affect the GTP[S] (guanosine 5'-[gamma-[35S]thio]triphosphate)-binding activity. Both C214A and C214W mutants serve as good substrates for pertussis toxin-catalysed ADP ribosylation, indicating that they interact well with betagamma subunits. Moreover, RGS4 protein, a GTPase-activating protein for Galpha(i1), cannot interact with Cys-214 mutants even in the presence of AlF4-, which induces the transition state of Galpha. In summary, our findings suggest that C214A or C214W are GTPase-deficient mutants and can functionally serve as constitutively active forms of Galpha(i1) in cells.
Thyrotropin and Adenosine 3′, 5′- Monophosphate Stimulate the Activity of the Ferritin-H Promoter (1990)

Fragments of the rat ferritin-H 5'-flanking region up to 1 kilobase in length were generated by the polymerase chain reaction using FRTL5 rat thyroid cell genomic DNA as template. Ferritin-H 5'-flanking region fragments of 219, 351, 666, and 1046 basepairs (bp), ligated up-stream to the reporter gene luciferase, were transiently transfected into FRTL5 thyroid cells and NIH-3T3 mouse fibroblasts. In both cell types, constitutive (nonstimulated) ferritin-H promoter activity increased progressively with constructs containing increasing lengths of 5'-flanking region. TSH or (Bu)2cAMP (dBcAMP) stimulation of FRTL5 cells transfected with the shorter (219 and 351 bp) ferritin-H 5'-flanking region fragments increased promoter activity 2- to 3-fold. However, with the longer DNA segments (666 and 1046 bp), the extent of TSH stimulation was less. Exposure of transfected NIH-3T3 cells to dBcAMP mimicked in all respects the effects of TSH and dBcAMP on ferritin-H promoter activity in FRTL5 cells. Transcription initiation sites in the luciferase reporter gene were unaffected by the length of the ferritin-H 5'-flanking region included in the construct or by dBcAMP stimulation. Plasmid constructs with 45 bp of the ferritin-H 5'-flanking region containing a potential cAMP response element did not reveal any promoter activity or dBcAMP responsiveness in this region. Gel shift mobility assays with the -219 bp ferritin-H 5'-flanking region fragment and NIH-3T3 nuclear proteins revealed specific protein-DNA interaction. Reduced DNA mobility was inhibited by excess unlabeled probe DNA, but not by DNA fragments corresponding to the recognition sites for a variety of known trans-activating factors.(ABSTRACT TRUNCATED AT 250 WORDS)
Computer Manufacturing Management Integrating Lean Six Sigma and Prognostic Health Management (2010)

Computer manufacturers have been applying Six Sigma for continuous quality improvement and Lean Manufacturing for reducing process waste in order to maximally meet customer requirements. However, top computer manufacturers are now realizing the design and production with advanced capability for early failure detection, fault diagnostic and prediction will significantly improve product life cycle performance and increase competitive advantages. In this paper, prognostic health management is proposed as a predictive management strategy centered by technological approach. Through integration with Lean Six Sigma, a raised computer manufacturing management performance can be achieved .
Freeze injection and compression molding of fine ceramic powder by using water binder. (1987)

To solve the problem that an extremely long debinding time is required before sintering in case of the ceramics powder injection molding process, the water binder is used for its easy debinding property in stead of polymer or wax binder and the shape fixing is done by freezing the binding water in the die cavity after compression forming.The vacuum freeze drying is applied for removing the water binder in order to prevent the cracking by the shrinkage of formed powder.