gebhart/patrepeval huggingface dataset:
Relocating a gene for herbicide tolerance: A chloroplast gene is converted into a nuclear gene (1988)

The chloroplast gene psbA codes for the photosynthetic quinone-binding membrane protein Q(B), which is the target of the herbicide atrazine. This gene has been converted into a nuclear gene. The psbA gene from an atrazine-resistant biotype of Amaranthus hybridus has been modified by fusing its coding region to transcription-regulation and transit-peptide-encoding sequences of a bona fide nuclear gene. The constructs were introduced into the nuclear genome of tobacco by using the Agrobacterium tumor-inducing (Ti) plasmid system, and the protein product of nuclear psbA has been identified in the photosynthetic membranes of chloroplasts. Recovery of atrazine-tolerant transgenic plants shows that the product of the transplanted gene functions in photosynthesis. These experiments show that it is possible to modify chloroplast-gene-specified functions via nuclear-genome transformation and also raise evolutionary questions.
Live cell lithography: Using optical tweezers to create synthetic tissue (2008)

We demonstrate a new method for creating synthetic tissue that has the potential to capture the three-dimensional (3D) complexity of a multi-cellular organism with submicron precision. Using multiple laminar fluid flows in a microfluidic network, we convey cells to an assembly area where multiple, time-shared optical tweezers are used to organize them into a complex array. The cells are then encapsulated in a 30 microm x 30 microm x 45 microm volume of photopolymerizable hydrogel that mimicks an extra-cellular matrix. To extend the size, shape and constituency of the array without loss of viability, we then step to an adjacent location while maintaining registration with the reference array, and repeat the process. Using this step-and-repeat method, we formed a heterogeneous array of E. coli genetically engineered with a lac switch that is functionally linked to fluorescence reporters. We then induced the array using ligands through a microfluidic network and followed the space-time development of the fluorescence to evaluate viability and metabolic activity.
Epitope Mapping of Antibodies to the C-Terminal Region of the Integrin β2 Subunit Reveals Regions that Become Exposed Upon Receptor Activation (2001)

The cysteine-rich repeats in the stalk region of integrin beta subunits appear to convey signals impinging on the cytoplasmic domains to the ligand-binding headpiece of integrins. We have examined the functional properties of mAbs to the stalk region and mapped their epitopes, providing a structure-function map. Among a panel of 14 mAbs to the beta(2) subunit, one, KIM127, preferentially bound to alpha(L)beta(2) that was activated by mutations in the cytoplasmic domains, and by Mn(2+). KIM127 also bound preferentially to the free beta(2) subunit compared with resting alpha(L)beta(2). Activating beta(2) mutations also greatly enhanced binding of KIM127 to integrins alpha(M)beta(2) and alpha(X)beta(2). Thus, the KIM127 epitope is shielded by the alpha subunit, and becomes reexposed upon receptor activation. Three other mAbs, CBR LFA-1/2, MEM48, and KIM185, activated alpha(L)beta(2) and bound equally well to resting and activated alpha(L)beta(2), differentially recognized resting alpha(M)beta(2) and alpha(X)beta(2), and bound fully to activated alpha(M)beta(2) and alpha(X)beta(2). The KIM127 epitope localizes within cysteine-rich repeat 2, to residues 504, 506, and 508. By contrast, the two activating mAbs CBR LFA-1/2 and MEM48 bind to overlapping epitopes involving residues 534, 536, 541, 543, and 546 in cysteine-rich repeat 3, and the activating mAb KIM185 maps near the end of cysteine-rich repeat 4. The nonactivating mAbs, 6.7 and CBR LFA-1/7, map more N-terminal, to subregions 344-432 and 432-487, respectively. We thus define five different beta(2) stalk subregions, mAb binding to which correlates with effect on activation, and define regions in an interface that becomes exposed upon integrin activation.
pRB family proteins are required for H3K27 trimethylation and Polycomb repression complexes binding to and silencing p16INK4a tumor suppressor gene (2007)

Genetic studies have demonstrated that Bmi1 promotes cell proliferation and stem cell self-renewal with a correlative decrease of p16(INK4a) expression. Here, we demonstrate that Polycomb genes EZH2 and BMI1 repress p16 expression in human and mouse primary cells, but not in cells deficient for pRB protein function. The p16 locus is H3K27-methylated and bound by BMI1, RING2, and SUZ12. Inactivation of pRB family proteins abolishes H3K27 methylation and disrupts BMI1, RING2, and SUZ12 binding to the p16 locus. These results suggest a model in which pRB proteins recruit PRC2 to trimethylate p16, priming the BMI1-containing PRC1L ubiquitin ligase complex to silence p16.
Ideal Schottky diodes on passivated silicon (1992)

Because of the complicated electronic and metallurgical properties of the metal-semiconductor interface, there is much controversy about the theoretical interpretation of experimental results on Schottky barrier heights. We present a new approch of barrier height measurements on a prototypical clean, abrupt and noninteracting system consisting of mercury contacts to hydrogen-passivated silicon surfaces. The resulting barrier to p-silicon is 0.9 V, totally at variance with all results presented for silicon Schottky barriers fabricated by standard metal deposition techniques. We believe this to be the first report in the limit of noninteracting metal contacts to silicon.
Low cancer prevalence in polyglutamine expansion diseases (2017)

There was a decreased cancer rate in PolyQ diseases despite high incidence of risk factors. Intriguingly, skin cancer incidence was higher, suggesting a crosstalk between neurodegeneration and skin tumorigenesis.
Detection of Isoforms Differing by a Single Charge Unit in Individual Cells (2016)

To measure protein isoforms in individual mammalian cells, we report single-cell resolution isoelectric focusing (scIEF) and high-selectivity immunoprobing. Microfluidic design and photoactivatable materials establish the tunable pH gradients required by IEF and precisely control the transport and handling of each 17-pL cell lysate during analysis. The scIEF assay resolves protein isoforms with resolution down to a single-charge unit, including both endogenous cytoplasmic and nuclear proteins from individual mammalian cells.
Writing Throughout the Curriculum: Why Law Schools Need It and How to Achieve It (1997)

I. Introduction II. Writing as a Tool for Analyzing and Applying Legal Authorities ... A. Using Writing to Diagnose Thinking Problems ... B. Using Writing to Promote Clear Thinking ... C. Using Writing-to-Learn Activities to Complement Traditional Teaching Methods III. Writing Skills as “Tools of the Trade” ... A. Acquainting Students with Functions and Forms of Professional Documents ... 1. Introducing Purposes and Audiences for Legal Writing ... 2. Providing Models of Effective Legal Writing ... B. Teaching Students to Produce Professional-Quality Documents IV. Writing as a Tool for Constructing Meaning ... A. Using Writing to Examine the Process of Interpreting Law and Fact ... B. Teaching Writing as an Interpretive Process ... 1. Telling the Client’s Story ... a. In a First-Year Legal Writing Class ... b. Throughout the Curriculum ... 2. Finding One’s Own Voice ... C. Using Writing to Encourage Self-Awareness and to Develop Professional Integrity V. Conclusion: What Is the “Ideal” Law School Writing Program?
Exploring the Relationships Between Hotel Management Courses and Industry Required Competencies (2002)

ABSTRACT Recently, higher education in Taiwan for the hospitality industry has grown dramatically. However, hospitality education is still considered a relative newborn in comparison with other programs. To develop effective programs, it would be appropriate to investigate competencies that influence career success in the hotel industry and the courses that nurture those important competencies. A researcher-developed survey instrument was used to collect data from 200 industry professionals. Instrument reliability and validity were reported. The results revealed the competencies relating to communication and adaptability most influenced career success. Moreover, Finance/Marketing/Personnel Management, Foreign Languages, and Communications & Quality Management curriculum dimensions were significantly related to competencies of “communication skills & adaptation to environmental changes.”
Expression of the Pycnoporus cinnabarinus laccase gene in Aspergillus niger and characterization of the recombinant enzyme (2002)

Pycnoporus cinnabarinus laccase lac1 gene was overexpressed in Aspergillus niger , a well‐known fungal host producing a large amount of homologous or heterologous enzymes for industrial applications. The corresponding cDNA was placed under the control of the glyceraldehyde‐3‐phosphate dehydrogenase promoter as a strong and constitutive promoter. The laccase signal peptide or the glucoamylase preprosequence of A. niger was used to target the secretion. Both signal peptides directed the secretion of laccase into the culture medium as an active protein, but the A. niger preprosequence allowed an 80‐fold increase in laccase production. The identity of the recombinant protein was further confirmed by immunodetection using Western blot analysis and N‐terminal sequencing. The molecular mass of the mature laccase was 70 kDa as expected, similar to that of the native form, suggesting no hyperglycosylation. The recombinant laccase was purified in a three‐step procedure including a fractionated precipitation using ammonium sulfate, and a concentration by ultrafiltration followed by a Mono Q column. All the characteristics of the recombinant laccase are in agreement with those of the native laccase. This is the first report of the production of a white‐rot laccase in A. niger .
The requirement for surveillance of HIV drug resistance within antiretroviral rollout in the developing world (2006)

Purpose of review To describe surveillance measures to inform HIV drug-resistance prevention, as part of the public health approach to antiretroviral therapy in developing countries. Recent findings Neither HIV drug-resistance transmission nor its emergence in treatment is routinely assessed in the developing world, but routine methods should be part of antiretroviral therapy scale-up. Mathematical modelling and experience in resource-rich countries suggest HIV drug-resistance transmission will increase as antiretroviral therapy coverage increases, but its rise will be limited initially. Transmission surveys should begin in geographic areas in each country where antiretroviral therapy coverage is widespread. Reports from resource-limited countries suggest that antiretroviral therapy programs are as effective as in resource-rich countries, which should limit HIV drug resistance if effectiveness is maintained with antiretroviral therapy expansion. Surveillance of HIV drug resistance emerging in treatment and other factors will support implementation of prevention measures on a population level. Summary Standardized surveillance of transmitted and treatment-associated HIV drug resistance is critical to the success of antiretroviral therapy expansion in developing countries. Routine assessment of prescribing practices, availability of and access to appropriate regimens for adults and children, antiretroviral drug supply continuity, and measures to prevent HIV transmission will supply critical information for HIV drug-resistance prevention.
CHAOTIC COMMUNICATION USING TIME-DELAYED OPTICAL SYSTEMS (1999)

We discuss experimental demonstrations of chaotic communication in several optical systems. In each, an erbium-doped fiber ring laser (EDFRL) produces chaotic fluctuations of light intensity onto which is modulated a message consisting of a sequence of pseudorandom digital bits. This combination of chaos and message propagates at a wavelength of ~ 1.5 microns through standard single-mode optical fiber from the transmitter to a receiver, where the message is recovered from the chaos. We present evidence of the high-dimensional nature of the chaotic waveforms and demonstrate chaotic communications through 35 km of single-mode optical fiber at up to 250 Mbit/s, a rate that is, at present, limited only by the speed of our detector electronics.
Complexes of tissue-type plasminogen activator and its serpin inhibitor plasminogen-activator inhibitor type 1 are internalized by means of the low density lipoprotein receptor-related protein/alpha 2-macroglobulin receptor. (1992)

Tissue-type plasminogen activator and urokinase are serine proteases secreted by many cell types that participate in biological processes, such as tissue restructuring, cell migration, and tumor metastasis. Clinically, these proteases are used to dissolve coronary fibrin clots that are the proximal causes of acute myocardial infarction. In vivo, the activity of these enzymes is controlled by plasminogen-activator inhibitors, members of the serpin family of protease inhibitors. This study shows that tissue-type plasminogen activator-inhibitor complexes bind in solution to low density lipoprotein receptor-related protein (LRP), a large heterodimeric ubiquitous membrane receptor. In cultured cells, endocytosis and degradation of these complexes is reduced by polyclonal antibodies directed against LRP and inhibited by a M(r) 39,000 protein that binds to LRP and inhibits its interaction with previously known ligands, including apolipoprotein E and alpha 2-macroglobulin. We propose a role for LRP in the clearance of plasminogen activator-inhibitor complexes that is analogous to its function in the endocytosis of alpha 2-macroglobulin-protease complexes.
On-chip 3D air-core microinductor for high-frequency applications using deformation of sacrificial polymer (2001)

A novel on-chip 3D air core micro-inductor, utilizing deformation of sacrificial thick polymer and conformal photoresist electrodeposition techniques, is reported. The bottom conductors are formed on silicon or glass substrate by metal electroplating through SU-8 polymeric mold. A thick SJR 5740 photoresist is then spun on and patterned to be a supporting mesa. Hard curing of such polymer mesa could significantly deform it into a cross-sectional bell-shape sacrificial core with graded profile in which is used to support top conductors formation. A layer of conformal electrodeposited photoresist (PEPR 2400) is then coated along the core's surface profile, patterned by standard optical lithography and filled up by metal electroplating. Finally, all polymeric molds including significantly deformed sacrificial core and electroplating bases are removed, resulting in an on-chip solenoid-type 3D air core micro-inductor. Since this new inductor has an air core and has only two contact points per turn, the core loss and equivalent series resistance are expected to be small, and hence, to give higher quality factor at high-frequency operation. Currently, high-frequency characterization of this on-chip inductor is under way.
COMBINED HISTOCOMPATIBILITY LEUKOCYTE ANTIGENMATCHED DONOR BONE MARROW AND RENAL TRANSPLANTATION FOR MULTIPLE MYELOMA WITH END STAGE RENAL DISEASE: THE INDUCTION OF ALLOGRAFT TOLERANCE THROUGH MIXED LYMPHOHEMATOPOIETIC CHIMERISM (1999)

This is the first report of the deliberate induction of mixed lymphohematopoietic chimerism after a nonmyeloablative preparative regimen to treat a hematological malignancy and to provide allotolerance for a solid organ transplant.
Neural Discharge and Local Field Potential Oscillations in Primate Motor Cortex During Voluntary Movements (1998)

The role of "fast," or gamma band (20-80 Hz), local field potential (LFP) oscillations in representing neuronal activity and in encoding motor behavior was examined in motor cortex of two alert monkeys. Using chronically implanted microwires, we simultaneously recorded LFPs and single or multiple unit (MU) discharge at a group of sites in the precentral gyrus during trained finger force or reaching movements, during natural reaching and grasping, and during quiet sitting. We evaluated the coupling of oscillations with task-related firing at the same site, the timing of oscillations with respect to the execution of trained and untrained movement, and the temporal synchrony of oscillations across motor cortical sites. LFPs and neural discharge were examined from a total of 16 arm sites (7 sites in 1 monkey and 9 in the other), each showing movement-related discharge modulation and arm microstimulation effects. In the trained tasks, fast LFP and MU oscillations occurred most often during a premovement delay period, ceasing around movement onset. The decrease in oscillation roughly coincided with the appearance of firing rate modulation coupled to the motor action. During this delay, LFP oscillations exhibited either "overlapping" or "mixed" relationships with the simultaneously recorded neural discharge at that site. Overlap was characterized by coincident epochs of increased neural discharge and LFP oscillations. For the mixed pattern, episodes of LFP oscillation typically coincided with periods of diminished firing but overlap also sometimes appeared. Both patterns occurred concurrently across motor cortex during preparation; LFP suppression with motor action was ubiquitous. Fast oscillations reappeared quickly upon transition from quiet sitting to resumption of task performance, indicating an association with task engagement, rather than the general motor inaction of the delay period. In contrast to trained movements, fast oscillations often appeared along with movement during untrained reaching, but oscillations occurred erratically and were not reliably correlated with elevated neural discharge. Synchronous oscillations occurred at sites as much as 5 mm apart, suggesting widespread coupling of neurons and LFP signals in motor cortex. Widespread coupling of oscillatory signals is consistent with the concept that temporal coding processes operate in motor cortex. However, because the relationship between neuronal discharge and the appearance of fast oscillations may be altered by behavioral condition, they must reflect a global process active in conjunction with motor planning or preparatory functions, but not details of motor action encoded in neuronal firing rate.
The Emergence of Computational Ecologies (2018)

The effective use of distributed computation is a challenging task, since the processes must obtain resources in a dynamically changing environment and must be designed to collaborate despite a variety of asynchronous and unpredictable changes. From a scientific point of view, the analogy between distributed computation and natural ecologies brings to mind the spontaneous appearance of organized behaviour in biological and social systems, where agents can engage in cooperating strategies while working on the solution of particular problems. The chapter describes a market-based computational ecosystem and a theory of distributed computation. The theory describes the collective dynamics of computational agents, while incorporating many of the features endemic to such systems, including distributed control, asynchrony, resource contention, and extensive communication among agents. The chapter provides an effective procedure for controlling chaos in distributed systems. It is based on a mechanism that rewards agents according to their actual performance.
Review: Overlapping and Distinct Mechanisms Regulating IRF-3 and IRF-7 Function (2002)

Recent molecular, biochemical, and gene disruption studies have demonstrated the essential role of interferon (IFN) regulatory factor-3, (IRF-3) and IRF-7 in the activation of type I IFN gene expression and the induction of the antiviral state. Both transcription factors share structural and functional properties, as well as a common mechanism of activation through C-terminal phosphorylation. The purpose of this review is to summarize recent investigations indicating that similar signalling pathways are likely involved in the activation of IRF-3 and IRF-7. Moreover, unique biochemical events, such as coactivator association and differential recognition of cis-acting elements, also illustrate the capacity of IRF-3 and IRF-7 to selectively regulate type I IFN and IFN-stimulated gene (ISG) expression.
Expression of c-Ets1 is associated with malignant potential in endometrial carcinoma (2000)

The authors' results show that c-Ets1 expression in endometrial carcinoma correlates with the malignant potential of this tumor.
Corneal Crosslinking and Visual Rehabilitation in Keratoconus in One Session Without Epithelial Debridement: New Technique (2010)

A new surgical technique for the treatment of keratoconus is presented. This technique combines a new corneal crosslinking method with implantation of a flexible full-ring implant into a "closed" corneal pocket via a narrow incision tunnel in 1 surgical session. Riboflavin is not applied in the form of eyedrops onto a corneal surface after epithelial removal but is instilled into the corneal pocket without the need for epithelial debridement. A case of advanced keratoconus treated in this manner is presented. Uncorrected visual acuity increased by 7 lines from 0.05 to 0.25, and the average central K reading decreased by 11 diopters. The haze seen during the early postoperative period diminished in the first month after surgery.
Persistent High Restenosis After Local Intrawall Delivery of Long-Acting Steroids Before Coronary Stent Implantation. (1998)

OBJECTIVE: This pilot study was performed to evaluate the feasibility and safety of intrawall delivery of long acting steroids before stent implantation, testing the efficacy of this treatment in reducing intimal hyperplasia in lesions at high risk for restenosis. METHODS: In 24 patients (40 lesions) local intrawall drug delivery of methylprednisolone acetate, using a new catheter device, was attempted before elective stent implantation. Treated lesions were compared to a matched control group. RESULTS: Lesions were classified AHA/ACC type C in 47% of cases, had a mean lesion length of 13.6 +/- 9.1 mm, and a mean vessel diameter of 2.85 +/- 0.44 mm. In 9 cases (25%) chronic total occlusions were treated. Methylprednisolone acetate (mean 60 +/- 23 mg) was delivered in 36 lesions (21 patients; delivery success 90%) in the remaining 4 lesions (10%) the delivery device did not cross the lesion. After drug delivery 46 stents were implanted (1.2 stent/lesion; stented segment length 30.1 +/- 18.8 mm) using high pressure for stent expansion (mean 16.4 +/- 3.1 atm). Intracoronary ultrasound guidance was used in 64% of cases. Procedural and in-hospital complications were: Two non Q wave myocardial infarctions (8%) and one (3%) subacute stent thrombosis. Angiographic follow-up was obtained in all 36 treated lesions (100%) and the angiographic restenosis rate (³ 50% diameter stenosis) was 39%. A reduction of the incidence of restenosis compared to the matched control group was not observed. CONCLUSIONS: Long acting steroids could be delivered locally with high success and low complication rates. The restenosis rate remained high in a subset of unfavorable lesions with high risk for restenosis.
Change with age of the refractive index gradient of the human ocular lens. (1995)

It has been observed that surface curvatures and thicknesses of the ocular lens increase with age, whereas other ocular dimensions apparently do not change, implying a trend toward myopia. This trend has not been observed. The authors' results are consistent with and strongly in support of the hypothesis that subtle index changes in the aging lens compensate to a large extent for changes in surface curvatures.