gebhart/patrepeval huggingface dataset:
Unix: The Complete Reference, Second Edition (2007)

The Definitive UNIX Resource--Fully Updated
Get cutting-edge coverage of the newest releases of UNIX--including Solaris 10, all Linux distributions, HP-UX, AIX, and FreeBSD--from this thoroughly revised, one-stop resource for users at all experience levels. Written by UNIX experts with many years of experience starting with Bell Laboratories, UNIX: The Complete Reference, Second Edition provides step-by-step instructions on how to use UNIX and take advantage of its powerful tools and utilities. 

Get up-and-running on UNIX quickly, use the command shell and desktop, and access the Internet and e-mail. You'll also learn to administer systems and networks, develop applications, and secure your UNIX environment. Up-to-date chapters on UNIX desktops, Samba, Python, Java Apache, and UNIX Web development are included. 

Install, configure, and maintain UNIX on your PC or workstation
Work with files, directories, commands, and the UNIX shell
Create and modify text files using powerful text editors
Use UNIX desktops, including GNOME, CDE, and KDE, as an end user or system administrator 
Use and manage e-mail, TCP/IP networking, and Internet services
Protect and maintain the security of your UNIX system and network
Share devices, printers, and files between Windows and UNIX systems
Use powerful UNIX tools, including awk, sed, and grep
Develop your own shell, Python, and Perl scripts, and Java, C, and C++ programs under UNIX
Set up Apache Web servers and develop browser-independent Web sites and applications


Table of contents

PART I – BASICS FOR LINUX/UNIX (revised)
Chapter 1. Background (revised)
Chapter 2. Getting Started (revised)
Chapter 3. Working with Files and Directories (revised)
Chapter 4. Working with Shells and Enhanced Shells (revised)
Chapter 5. Text Editing (revised)
Chapter 6. The Desktop: GNOME (new)
Chapter 7. CDE and other Desktops (new)
PART II – USER NETWORKING
Chapter 8. Electronic Mail (revised)
Chapter 9. TCP/IP and other Basic Networking Protocols (revised)
Chapter 10. Using the Internet (revised)
PART III – SYSTEM ADMINISTRATION
Chapter 11. Processes and Scheduling (revised)
Chapter 12. Security and Authentication (revised)
Chapter 13. Basic System Administration (revised)
Chapter 14. Advanced System Administration (revised)
PART IV – NETWORK ADMINISTRATION
Chapter 15. Clients and Servers (revised)
Chapter 16. Administering the Network (revised)
Chapter 17. Using UNIX and Windows Together: SAMBA and other Integration Tools (revised)
PART V - TOOLS
Chapter 18. Filters and Utilities (revised)
Chapter 19. Shell Programming (revised)
Chapter 20. awk and sed (revised) 
Chapter 21. Perl (revised)
Chapter 22. Python and PHP (new)
Chapter 23. Developing Applications (revised)
Chapter 24. Overview of Java (revised)
PART VI – ENTERPRISE SOLUTIONS
Chatper 25. UNIX Applications and Middleware (revised)
Chatper 26. Databases (new)
Chapter 27. Developing Web Applications and Running a Website (new)
VII – APPENDICES
APPENDIX A. HOW TO FIND OUT MORE (revised)
APPENDIX B. COMMAND SUMMARIES(revised)
Loss of nuclear poly(A)-binding protein 1 causes defects in myogenesis and mRNA biogenesis (2009)

The nuclear poly(A)-binding protein 1 (PABPN1) is a ubiquitously expressed protein that plays a critical role in polyadenylation. Short expansions of the polyalanine tract in the N-terminus of PABPN1 lead to oculopharyngeal muscular dystrophy (OPMD), which is an adult onset disease characterized by eyelid drooping, difficulty in swallowing and weakness in the proximal limb muscles. Although significant data from in vitro biochemical assays define the function of PABPN1 in control of poly(A) tail length, little is known about the role of PABPN1 in mammalian cells. To assess the function of PABPN1 in mammalian cells and specifically in cells affected in OPMD, we examined the effects of PABPN1 depletion using siRNA in primary mouse myoblasts from extraocular, pharyngeal and limb muscles. PABPN1 knockdown significantly decreased cell proliferation and myoblast differentiation during myogenesis in vitro. At the molecular level, PABPN1 depletion in myoblasts led to a shortening of mRNA poly(A) tails, demonstrating the cellular function of PABPN1 in polyadenylation control in a mammalian cell. In addition, PABPN1 depletion caused nuclear accumulation of poly(A) RNA, revealing that PABPN1 is required for proper poly(A) RNA export from the nucleus. Together, these experiments demonstrate that PABPN1 plays an essential role in myoblast proliferation and differentiation, suggesting that it is required for muscle regeneration and maintenance in vivo.
Photometric Inline Monitoring of Pigment Concentration in Highly Filled Lacquers (2020)

Abstract Der Einsatz von faseroptischen Rückstreusensoren zur Inline‐Überwachung der Partikelkonzentration in hochgefüllten Dispersionen und Lacksystemen wird dargestellt. Durch die Miniaturisierung des Abstandes zwischen Sender‐ und Empfängerfaser auf &lt; 600 µm kann das eingetragene Licht auch hohe Dispersphasenanteile von bis zu 60 % durchdringen. Aufgrund der Messanordnung finden sich sowohl Transmissions‐ als auch Streueinflüsse im resultierenden Signal. Es folgt eine mögliche Beschreibung der sich ergebenden nichtlinearen Messkurve mittels eines vereinfachten Modells.
Progress towards in vivo glucose sensing with a ferrocene-mediated amperometric enzyme electrode. (1988)

A range of miniature, amperometric enzyme electrodes have been constructed using the principle of mediated transfer of electrons. Ferrocene, or one of its derivatives, can be used in conjunction with immobilised glucose oxidase to produce sensors which are linear to at least 20 mmol/l glucose, have fast response times, are relatively oxygen insensitive and are suitable for implantation studies. In preliminary experiments in non-diabetic pigs, electrode responses followed blood responses, although mean tissue levels were about one fifth of those in blood. The ferrocene technology thus appears to be suitable for adaptation to the construction of implantable glucose electrodes for use in diabetic man.
Albumin Rescues Ocular Epithelial Cells from Cell Death in Dry Eye (2007)

Albumin showed a therapeutic effect in dry eye model rats. This efficacy may be related to the suppression of apoptosis by albumin.
Process design and costing of an air-contactor for air-capture (2011)

Carbon Engineering (CE) has developed an air-contactor design, specifically optimized to the challenge of efficiently removing CO2 from atmospheric air. CE's air-contactor design is based on the wet-scrubbing method, where air is brought into contact with an alkali hydroxide CO2-absorbing liquid solution. This is a similar process to that carried out in absorption or reactor towers commonly used in the chemical processing industry, but unique constraints posed by the challenge of removing CO2 from atmospheric air have led CE to a number of original, innovative, and proprietary design modifications to these existing technologies. These key differences have led CE to depart from traditional chemical industry practice involving packed reactor towers, and to develop an intermittently- wetted air-contactor with cross-flow slab geometry. This design has as much in common with induced draft cooling towers as with chemical reactor towers. Design has been tested in a 5 m tall packed tower prototype and detailed tests of packing performance have been performed in a laboratory system that enables us to control CO2, air velocity, relative humidity while accurately measuring packing performance. In addition to CE's on-going in-house engineering and experimental evaluations, the structural design and cost estimation of the air-contactor system was performed by an independent Engineering, Procurement and Construction (EPC) firm (SolTech Projects Inc., Calgary, Alberta). The cost estimate produced by this EPC firm forms a conservative upper bound on the cost of the air-contactor because it is based on 2008/09 Alberta, Canada construction and labour costs, which were among the highest in the world. The EPC firm collected quotes from vendors for major equipment and components, and the total system cost was estimated using standard engineering cost-evaluation procedures. The total estimated cost of the air-contacting system, evaluated using conservative labour and energy rates as mention equates to $80/tonne- CO2 and CE has identified specific areas of research to decrease this cost to $49/tonne- CO2.
Identification of phenocopies improves prediction of targeted therapy response over DNA mutations alone (2022)

DNA mutations in specific genes can confer preferential benefit from drugs targeting those genes. However, other molecular perturbations can "phenocopy" pathogenic mutations, but would not be identified using standard clinical sequencing, leading to missed opportunities for other patients to benefit from targeted treatments. We hypothesized that RNA phenocopy signatures of key cancer driver gene mutations could improve our ability to predict response to targeted therapies, despite not being directly trained on drug response. To test this, we built gene expression signatures in tissue samples for specific mutations and found that phenocopy signatures broadly increased accuracy of drug response predictions in-vitro compared to DNA mutation alone, and identified additional cancer cell lines that respond well with a positive/negative predictive value on par or better than DNA mutations. We further validated our results across four clinical cohorts. Our results suggest that routine RNA sequencing of tumors to identify phenocopies in addition to standard targeted DNA sequencing would improve our ability to accurately select patients for targeted therapies in the clinic.
Silicon molecular beam epitaxy with simultaneous ion implant doping (1980)

Silicon epitaxial layers have been made with virtually any doping profile by combining molecular beam epitaxial growth with simultaneous ion implant doping. Arsenic ions (As+) accelerated to energies between 400 and 800 eV have shown a high sticking coefficient on the heated silicon surface. Growth conditions have been defined at which epitaxial films with bulk characteristics are obtained.
Transgene-induced production of IL-4 alters the development and collagen expression of T helper cell 1-type pulmonary granulomas (1997)

A number of complex mechanisms regulate the size and cellularity of an Ag-dependent granulomatous reaction and their accompanying cytokine production profiles. In the present study, Th1 (purified protein derivative (PPD)) and Th2 (schistosome egg Ag)-type granulomas were established to examine the role of IL-4 in lesion development and procollagen type III expression. PPD-sensitized mice were transfected via the airway with an adenovirus construct containing an IL-4 cDNA cassette, and the lungs were embolized with sized Ag-coated Sepharose beads. Granuloma development in response to the PPD bead challenge in control mice primarily consisted of mononuclear cells. In contrast, the overexpression of IL-4 in the IL-4 adenovirus-transfected animals demonstrated a significant increase in cellularity, size, procollagen type III expression, and accumulation of eosinophils. Analysis of mRNA and protein within the lung demonstrated significant expression of IL-4 in only the IL-4 adenovirus-transfected animals. The granuloma lesion size was significantly increased in the IL-4 adenovirus-transfected animals on days 2 and 5, reaching an approximate 50% increase compared with the control groups. Furthermore, procollagen type III mRNA expression was increased in the IL-4 adenovirus-transfected, PPD bead-embolized lungs. In contrast, when IL-4 was neutralized during Th2-type schistosome egg Ag bead granulomas, a decrease in procollagen type III was observed. These data indicate that the progression of certain granulomas may be regulated by the production of IL-4, thus altering the cellularity, size, and matrix composition of the inflammatory response.
Nitrogen‐Rich Plasma‐Polymer Films for Biomedical Applications (2007)

Abstract Low‐pressure plasma co‐polymerisation of binary gas mixtures of ethylene and ammonia was investigated in order to deposit N‐rich plasma polymer coatings for biomedical applications. Deposition kinetics and relevant surface characteristics were investigated as a function of r.f. power, gas pressure, and NH 3 /C 2 H 4 ratio. Physico‐chemical properties of the coatings were determined by surface‐sensitive techniques: for example, total nitrogen concentrations up to 40 at.‐% were measured by XPS, while those of primary amines were determined by chemical derivatisation followed by XPS analysis. L‐PPE:N films were further characterised by UV‐vis and IR spectroscopic ellipsometry and by CAG. magnified image
Strut fracture mechanisms of the Björk-Shiley convexo-concave heart valve. (1999)

Investigations of convexo-concave (C/C) valve outlet strut fractures (OSFs) were initially confounded by knowledge that the strut was subject to bending forces in arresting the opening disc. Pulse duplicator studies subsequently showed that closing loads were all born by the inlet strut, along with an understandable focus on the nature of the welds, where most fractures occurred. As observations of explanted valves accumulated, certain features pointed to unusual closing loads that might be contributory factors, but these hypothetical forces could not be verified. Epidemiological extrapolations and case-matched control studies have shown that certain valve and patient characteristics were each associated independently with increased OSF risk, leading to clinically valuable risk stratification, but little additional understanding of why OSFs continued to occur. Detection of the causative, highly transient (< 0.5 ms), outlet-strut-tip impacts due to closing disc over-rotation that have almost ten times the force of disc opening, and the capability of inducing leg-base bending stresses beyond the strut wire's fatigue endurance limit had to await the development of computer-controlled pulse duplicators and strut-leg strain gaging. Exercised young animals easily achieved such strut loading, but most human patients would probably have more difficulty. The actual OSF mechanism is a long-term, valve-patient interaction that requires the concurrence of susceptible valve geometry and sufficient ventricular contractility potential to develop the isovolumic, high dP/dt needed for forceful disc over-rotation. Critical strut tip loading must then occur often enough to fatigue fracture both strut legs within the patient's lifetime with the valve.
Cellular Content of UDP-N-acetylhexosamines Controls Hyaluronan Synthase 2 Expression and Correlates with O-Linked N-Acetylglucosamine Modification of Transcription Factors YY1 and SP1 (2011)

Hyaluronan, a high molecular mass polysaccharide on the vertebrate cell surface and extracellular matrix, is produced at the plasma membrane by hyaluronan synthases using UDP-GlcNAc and UDP-GlcUA as substrates. The availability of these UDP-sugar substrates can limit the synthesis rate of hyaluronan. In this study, we show that the cellular level of UDP-HexNAc also controls hyaluronan synthesis by modulating the expression of HAS2 (hyaluronan synthase 2). Increasing UDP-HexNAc in HaCaT keratinocytes by adding glucosamine down-regulated HAS2 gene expression, whereas a decrease in UDP-HexNAc, realized by mannose treatment or siRNA for GFAT1 (glutamine:fructose-6-phosphate amidotransferase 1), enhanced expression of the gene. Tracing the UDP-HexNAc-initiated signal to the HAS2 promoter revealed no change in the binding of STAT3, NF-κB, and cAMP response element-binding protein, shown previously to mediate growth factor and cytokine signals on HAS2 expression. Instead, altered binding of SP1 and YY1 to the promoter correlated with cellular UDP-HexNAc content and inhibition of HAS2 expression. siRNA silencing of YY1 and SP1 confirmed their inhibitory effects on HAS2 expression. Reduced and increased levels of O-GlcNAc-modified SP1 and YY1 proteins were associated with stimulation or inhibition of HAS2 expression, respectively. Our data are consistent with the hypothesis that, by regulating the level of protein O-GlcNAc modifications, cellular UDP-HexNAc content controls HAS2 transcription and decreases the effects on hyaluronan synthesis that would result from cellular fluctuations of this substrate.
Subject‐specific segregation of functional territories based on deep phenotyping (2020)

Functional magnetic resonance imaging (fMRI) has opened the possibility to investigate how brain activity is modulated by behavior. Most studies so far are bound to one single task, in which functional responses to a handful of contrasts are analyzed and reported as a group average brain map. Contrariwise, recent data-collection efforts have started to target a systematic spatial representation of multiple mental functions. In this paper, we leverage the Individual Brain Charting (IBC) dataset-a high-resolution task-fMRI dataset acquired in a fixed environment-in order to study the feasibility of individual mapping. First, we verify that the IBC brain maps reproduce those obtained from previous, large-scale datasets using the same tasks. Second, we confirm that the elementary spatial components, inferred across all tasks, are consistently mapped within and, to a lesser extent, across participants. Third, we demonstrate the relevance of the topographic information of the individual contrast maps, showing that contrasts from one task can be predicted by contrasts from other tasks. At last, we showcase the benefit of contrast accumulation for the fine functional characterization of brain regions within a prespecified network. To this end, we analyze the cognitive profile of functional territories pertaining to the language network and prove that these profiles generalize across participants.
The role of HER-2 expression in predicting response to therapy in breast cancer. (2000)

HER-2 expression may have predictive value regarding response to therapeutic interventions in breast cancer. A number of reports describe the interaction of HER-2 overexpression and tamoxifen, but data are inconclusive. Chemotherapy trials have supported an interaction between HER-2 overexpression and chemotherapy sensitivity (cyclophosphamide/methotrexate/5-fluorouracil resistance and doxorubicin sensitivity) which is compelling. More recently, HER-2 has been the target for Food and Drug Administration-approved antibody therapy, trastuzumab (Herceptin; Genentech, Inc, South San Francisco, CA). The Clinical Trials Assay, a scoring system for tumor material, has been used successfully in the trastuzumab clinical development program. As many of the early studies evaluating the role of HER-2 were retrospective, controlled prospective studies are needed to best determine the value of trastuzumab in the adjuvant clinical setting.
Resource allocation for MIMO orthogonal relay channels with finite-rate feedback (2009)

Multiple antennas and relay can improve spectral efficiency of a network. Half duplex relay channels employing decode-and-forward and total power constraint are considered in this work. The resource includes power and time for the receive and transmit stages of the relay. Resource allocation algorithm is designed in order to maximize an achievable rate. The source and the relay nodes are assumed to have partial channel state information (CSI) obtained through finite-rate feedback from relay and/or destination. The full-blown problem is stated and the result of a special case of orthogonal transmission is presented. The transmitters use the simple power on/off precoding with constant number of on-beams while the precoding matrices are chosen according to quantization on Grassmann manifolds. An earlier analytical result on finite rate feedback is employed in the resource allocation algorithm. The complicated expressions of the achievable rates and the non-convexity of the problem make the optimal resource allocations hard to obtain and analyze. Iterative and near optimal resource allocation algorithm is presented. Numerical results are provided to show the benefits of finiterate feedback by comparison of the achievable rates of the relay channel, two-hop transmission and the direct transmission.
Adhesives for optical devices (2002)

Three types of UV-curable adhesives, a room temperature curing sealant and a hot-melt adhesive for the fabrication of optical communications devices were developed. (1) Using new epoxies, acrylates and vinyl sulfide containing fluorine, bromine and sulfur, the refractive indices of UV-curable transparent adhesives can be controlled, in the range 1.41-1.70 within /spl plusmn/0.005 with a high light transmittance of 80-90% at a wavelength of 1.3 /spl mu/m. They possess an excellent refractive index matching that of optical glass and optical fibers. They have high adhesive strength and good durability. (2) The UV-curable precision adhesive has an extremely low volume shrinkage of 1.2% during curing and the cured adhesive has a low thermal expansion coefficient of <2/spl times/10/sup -5///spl deg/C. Therefore, they can be used in the fabrication of optical devices that require sub-micron positioning accuracy. (3) The UV-curable thermal-resistant adhesive exhibits a high glass transition temperature of more than 200/spl deg/C. This adhesive has applications in the assembly of optical components that require higher heat-resistance. (4) The water permeability of the moisture-protected adhesive sealant is an extremely small 8/spl times/10/sup -9/ cc cm/cm/sup 2//cmHg/sec at a high temperature of 75/spl deg/C. The optical excess loss of sealing fiber due to the microbending during curing and temperature cycling (+85/spl deg/C to -40/spl deg/C) is negligibly small (less than 0.01 dB). (5) The water-resistant hot-melt adhesive for reinforcing optical-fiber splices applied to quartz glass by hot-press for 3 minutes at 130/spl deg/C provides excellent adhesion. The peel strength is maintained for over one year after immersion in water of 60/spl deg/C. These qualities of the developed UV-curable adhesives and the new sealants are advantageous for achieving low-cost and high reliability optical devices.
Modeling I/O Interference in Data Intensive Map-Reduce Applications (2012)

Map-Reduce is a popular framework for very large-scale data mining and processing. Recently, some works have attempted to model the behavior of Map-Reduce, but these existing models ignore the non-linearity of disk I/O performance under contention, which is a critical aspect of estimating the performance of data intensive applications. Understanding I/O interference between tasks running on the same node is critical in optimizing task scheduling for improved resource utilization. In this paper, we present a model to estimate the I/O behavior of Map-Reduce applications that can be used to achieve these goals.