gebhart/patrepeval huggingface dataset:
Analysis of shared memory misses and reference patterns (2002)

Shared bus computer systems permit the relatively simple and efficient implementation of cache consistency algorithms, but the shared bus is a bottleneck which limits performance. False sharing can be an important source of unnecessary traffic for invalidation-based protocols, elimination of which can provide significant performance improvements. For many multiprocessor workloads, however, most misses are true sharing plus cold start misses. Regardless of the cause of cache misses, the largest fraction of bus traffic are words transferred between caches without being accessed, which we refer to as dead sharing. We establish here new methods for characterizing cache block reference patterns, and we measure how these patterns change with variation in workload and block size. Our results show that 42 percent of 64-byte cache blocks are invalidated before more than one word has been read from the block and that 58 percent of blocks that have been modified only have a single word modified before an invalidation to the block occurs. Approximately 50 percent of blocks written and subsequently read by other caches show no use of the newly written information before the block is again invalidated. In addition to our general analysis of reference patterns, we also present a detailed analysis of dead sharing for each shared memory multiprocessor program studied. We find that the worst 10 blocks (based on most total misses) from each of our traces contribute almost 50 percent of the false shearing misses and almost 20 percent of the true sharing misses (on average). A relatively simple restructuring of four of our workloads based on analysis of these 10 worst blocks leads to a 21 percent reduction in overall misses and a 15 percent reduction in execution time. Permitting the block size to vary (as could be accomplished with a sector cache) shows that bus traffic can be reduced by 88 percent (for 64-byte blocks) while also decreasing the miss ratio by 35 percent.
Insulin Content and Insulinogenesis by the Perfused Rat Pancreas: Effects of Long Term Glucose Stimulation (1986)

The dynamic response of the perfused pancreas differed between pancreases from fed and fasted rats. Insulin secretion was significantly lower in pancreases from fasted rats during the first 40 min of perfusion at glucose levels of 200 and 300 mg/dl. Thereafter, from 40-90 min, insulin secretion was similar by pancreases from both fed and fasted rats. The typical biphasic insulin secretory profile, consisting of a transient spike of insulin secretion followed by a slowly rising secretory phase, was observed in pancreases from fasted rats. In contrast, the transition from first to second phase secretion was accelerated in pancreases from fed rats. This suggests that transport of intracellular insulin stores may be accentuated due to the fact that insulinogenic sites (e.g. Golgi) in pancreases from fed rats may be fully primed for optimal secretion. Total pancreatic insulin measurements support this concept. Total pancreatic insulin content was determined under fed and 24-h fasted conditions after various times of perfusion (0, 60, and 90 min and 6 h) and in response to various glucose levels (0, 200, and 300 mg/dl). Fasting resulted in a significant decrease in insulin content at zero time compared with pancreases from fed rats (39.2 +/- 2.4 vs. 61.6 +/- 9.8 micrograms). In the fed rat pancreases, total insulin content decreased slightly after a 60-min glucose stimulus of 300 mg/dl, but returned to the basal level after 90 min and remained at that level during a 6-h period of perfusion. In the fasted state, insulin content remained constant as a function of time until 60 min, but increased by 90 min to a level comparable to that in pancreases from fed rats. The response to lower levels of glucose stimulation (200 mg/dl) was qualitatively similar by pancreases from fed and fasted rats compared to the response to a higher glucose dose (300 mg/dl), except that secretion was less. Insulin content remained relatively constant for periods of perfusion up to 60 min. Insulinogenesis (defined as de novo synthesis and conversion of existing preproinsulin and proinsulin to insulin, less intracellular degradation of insulin) was increased as a function of glucose concentration and differed temporally as a function of the food intake of the animal. At no time of perfusion with any level of glucose stimulation did the insulin content exceed the zero time value in pancreases from fed rats. This suggests that insulin secretion is the rate-limiting step for insulinogenesis.
Selection of Transfected Mammalian Cells (1997)

Analysis of gene function frequently requires the formation of mammalian cell lines that contain the studied gene in a stably integrated form. Approximately one in 10(4) cells in a transfection will stably integrate DNA (the efficiency can vary depending on the cell type). Therefore, a dominant, selectable marker is used to permit isolation of stable transfectants. In the first part of this unit, the procedure for determining selection conditions and the resulting stable transfection is presented and the most commonly used selectable markers are discussed. The second protocol includes conditions for thirteen markers commonly used for selection of mammalian cells. A third protocols describes selection of transfected cells from the total population soon after transfection with plasmids that express both the gene of interest and a selection tag. Optimization of transfection conditions can be facilitated by a simple staining assay detailed in a support protocol.
Static and Dynamic Error Vector Magnitude Behavior of 2.4-GHz Power Amplifier (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This paper presents error vector magnitude (EVM) behavior under two different modes of a reference voltage <formula formulatype="inline"><tex>$({ V}_{\rm ref})$</tex></formula>; one is a static EVM with a constant <formula formulatype="inline"><tex>${ V}_{\rm ref}$</tex></formula> and the other is a dynamic EVM with a pulsed <formula formulatype="inline"><tex>${ V}_{\rm ref}$</tex></formula>. A 2.4-GHz two-stage power amplifier (PA) is implemented by GaAs HBT technology to investigate EVM behavior for IEEE 802.11 g wireless local area network application. A square wave pulse with the duty cycle of 50% is applied as <formula formulatype="inline"><tex>${ V}_{\rm ref}$</tex> </formula> for dynamic operation mode. </para>
ChemInform Abstract: New Base‐Labile Amino‐Protective Groups for Peptide Synthesis. (1989)

Abstract The stable succinimido carbonate (IV) is recommended for the introduction of the new protecting group Mpc.
On scalability of software-defined networking (2013)

In this article, we deconstruct scalability concerns in software-defined networking and argue that they are not unique to SDN. We explore the often voiced concerns in different settings, discuss scalability trade-offs in the SDN design space, and present some recent research on SDN scalability. Moreover, we enumerate overlooked yet important opportunities and challenges in scalability beyond the commonly used performance metrics.
P-OTX: a PIT-1-interacting homeodomain factor expressed during anterior pituitary gland development. (1996)

A novel OTX-related homeodomain transcription factor has been identified on the basis of its ability to interact with the transactivation domain of the pituitary-specific POU domain protein, Pit-1. This factor, referred to as P-OTX (pituitary OTX-related factor), is expressed in primordial Rathke's pouch, oral epithelium, first bronchial arch, duodenum, and hindlimb. In the developing anterior pituitary, it is expressed in all regions from which cells with distinct phenotypes will emerge in the mature gland. P-OTX is able to independently activate and to synergize with Pit-1 on pituitary-specific target gene promoters. Therefore, P-OTX may subserve functions in generating both precursor and specific cell phenotypes in the anterior pituitary gland and in several other organs.
A calcium-dependent antibody for identification and purification of recombinant proteins. (1989)

We report a straightforward methodology for purification of recombinant proteins by incorporating a short hydrophilic peptide marker segment at their N-termini. A calcium-dependent antibody that reacts primarily with the first three amino acids of this peptide segment was used to affinity purify the fusion proteins in a single chromatographic step. The marker peptide could subsequently be removed by proteolysis with the enzyme enterokinase.
Organization of the Epstein-Barr virus DNA molecule. III. Location of the P3HR-1 deletion junction and characterization of the NotI repeat units that form part of the template for an abundant 12-O-tetradecanoylphorbol-13-acetate-induced mRNA transcript (1983)

A 1,400-base-pair (bp) region within the BamHI H fragment of Epstein-Barr virus (EBV) (B95-8) DNA consists of a cluster of tandemly duplicated direct repetitions characterized by single sites for the NotI restriction endonuclease. Nucleotide sequencing revealed a 125-bp repeat unit of 84% guanine-plus-cytosine content which is theoretically capable of extensive secondary structure formation. The flanking sequences adjacent to the NotI repeat cluster contained an additional 38-bp portion of repeat unit DNA, thus establishing that EBV(B95-8) contains a nonintegral number of NotI repeats totalling 11.3 copies. Restriction site mapping of the homologous cloned BamHI "H" fragment from the nontransforming EBV (P3HR-1) isolate revealed that a contiguous 6,650-bp region including the entire NotI repeat cluster has been deleted from the BamHI-H, -Y, and -W regions of the P3HR-1 genome. By nucleotide sequencing across the novel junction, we have precisely identified the P3HR-1 deletion boundaries in BamHI-H and the internal repeat and suggest that a complex pattern of direct and inverted partial DNA homologies may have been involved in the original recombination event. The cloned BamHI H fragment and isolated NotI repeat unit have also been used as probes to detect homologous mRNA transcripts in the B95-8 and Raji cell lines of EBV-transformed lymphoblasts. These experiments showed that the NotI repeats form part of the template for a polyadenylated 2.5-kilobase mRNA transcript which becomes much more abundant after 12-O-tetradecanoyl-phorbol-13-acetate treatment of the cultures. The direction of transcription of this mRNA and the nucleotide sequence of most of its template and 5' flanking regions have been determined. The probable promoter for the 2.5-kilobase mRNA initiates transcription efficiently in an in vitro assay and contains several TAATGA-like elements that may be indicative of herpesvirus immediate-early class promoters. The need to repress expression of this gene during latency suggests a possible novel regulatory role for tandem repeat structures inside a eucaryotic virus transcription unit. The deletion in EBV(P3HR-1), which has been associated with the loss of lymphocyte "immortalizing" capacity in this isolate, eliminates part of the coding region as well as the NotI repeats from the 2.5-kilobase mRNA transcript, but the promoter and proximal 340-bp portions of the template remain.
Computing visual correspondence with occlusions using graph cuts (2002)

Several new algorithms for visual correspondence based on graph cuts have recently been developed. While these methods give very strong results in practice, they do not handle occlusions properly. Specifically, they treat the two input images asymmetrically, and they do not ensure that a pixel corresponds to at most one pixel in the other image. In this paper, we present a new method which properly addresses occlusions, while preserving the advantages of graph cut algorithms. We give experimental results for stereo as well as motion, which demonstrate that our method performs well both at detecting occlusions and computing disparities.
Kinetic role of nonnative species in the folding of bovine pancreatic trypsin inhibitor. (1992)

We have shown previously that during the oxidative folding of bovine pancreatic trypsin inhibitor only intermediates with native disulfide bonds are well populated. Nevertheless, these studies also confirmed the earlier conclusion [Creighton, T. E. (1977) J. Mol. Biol. 113, 275-293] that the rate-limiting transition in the kinetically preferred route for folding involves intramolecular disulfide bond rearrangements. Consequently, intermediates with nonnative disulfide bonds must form transiently during folding. Two specific nonnative species, denoted [30-51; 5-14] and [30-51; 5-38], in which numbers indicate residues participating in a disulfide bond, can be detected at low levels in kinetic folding experiments with bovine pancreatic trypsin inhibitor. By working with purified reversibly trapped intermediates, the role of these two nonnative species has been examined directly. These species are found to be in relatively rapid exchange with each other and with an initially formed native two-disulfide intermediate [30-51; 14-38]. Thus, the low abundance of the two nonnative species detected in kinetic folding experiments reflects primarily their low thermodynamic stability as compared to this native intermediate. To a small extent, these nonnative species form the productive native intermediate [30-51; 5-55], which is the immediate precursor to the native protein. However, an equal amount of [5-55; 14-38], a nonproductive dead-end intermediate, is also produced. Thus, the nonnative species detected during the folding of bovine pancreatic trypsin inhibitor are not committed to forming the productive native intermediate, nor do they serve to direct folding specifically toward a productive route.
Human and Mouse CD137 Have Predominantly Different Binding CRDs to Their Respective Ligands (2014)

Monoclonal antibodies (mAbs) to CD137 (a.k.a. 4-1BB) have anti-tumor efficacy in several animal models and have entered clinical trials in patients with advanced cancer. Importantly, anti-CD137 mAbs can also ameliorate autoimmunity in preclinical models. As an approach to better understand the action of agonistic and antagonistic anti-CD137 mAbs we have mapped the binding region of the CD137 ligand (CD137L) to human and mouse CD137. By investigating the binding of CD137L to cysteine rich domain II (CRDII )and CRDIII of CD137, we found that the binding interface was limited and differed between the two species in that mouse CD137L mainly combined with CRDII and human CD137L mainly combined with CRDIII.
Neuroprotective effects of tetramethylpyrazine on hydrogen peroxide‐induced apoptosis in PC12 cells (2006)

In the present study, we investigated the effects of tetramethylpyrazine (TMP) on hydrogen peroxide (H2O2)-induced apoptosis in PC12 cells. The apoptosis in H2O2-induced PC12 cells was accompanied by a decrease in Bcl-2/Bax protein ratio, release of cytochrome c to cytosol and the activation of caspase-3. TMP not only suppressed the down-regulation of Bcl-2, up-regulation of Bax and the release of mitochondrial cytochrome c to cytosol, but also attenuated caspase-3 activation and eventually protected against H2O2-induced apoptosis. These results indicated that TMP blocked H2O2-induced apoptosis by the regulation of Bcl-2 family members, suppression of cytochrome c release, and caspase cascade activation in PC12 cells.
Consensual Modifications of the Rules of Evidence: The Limits of Party Autonomy in an Adversary System (2001)

In the Anglo-American legal tradition, we have a distinctive adversary system. The distinctiveness lies in its allocation to the adversaries in a dispute the basic responsibility for discovering, marshalling, and presenting the facts of the case to the decision maker, either judge or jury, rather than assigning these tasks to a nonpartisan official. Parties to litigation are, for the most part, given great latitude in the manner in which they choose to assert their rights in court. The rules of evidence, which are themselves part and parcel of the adversary system, generally also operate upon the principle of party responsibility. This responsibility is most clearly embodied in the so-called contemporaneous objection rule, which requires the party wishing to see a rule of evidence enforced to lodge an objection as soon as an impending violation of the rule is reasonably to be anticipated. Several policies maintain the repute of the judicial system by insuring that its procedures comport with contemporary perceptions of rationality, preserving the essential structure and efficiency of the common law fact-finding process, enforcing rules intended to control areas in which the parties are prone to a mutual tendency toward partisan excess, and protecting the rights of third persons not directly involved in the litigation. A more specific recognition of the relatively few rules of evidence that should remain immune from party control will permit the adversary system to function with greater efficiency, as both adversaries and trial courts can more confidently realize the benefits of agreements designed to streamline and reduce the scope of litigation.
Diethylaminosulfur Trifluoride (DAST) (2006)

This feature focuses on a reagent chosen by a postgraduate, highlighting the uses and preparation of the reagent in current
A reservation-based algorithm for scheduling both periodic and aperiodic real-time tasks (1995)

This paper considers the problem of scheduling both periodic and aperiodic tasks in real-time systems. A new algorithm, called reservation-based (RB), is proposed for ordering the execution of real-time tasks. This algorithm can guarantee all periodic-task deadlines while minimizing the probability of missing aperiodic-task deadlines. Periodic tasks are scheduled according to the rate monotonic priority algorithm (RMPA), and aperiodic tasks are scheduled by utilizing the processor time left unused by periodic tasks in each unit cycle. The length, u, of a unit cycle is defined as the greatest common divisor of all task periods, and a task is assumed to be invoked at the beginning of a unit cycle. For a set S of periodic tasks, the RB algorithm reserves a fraction R/sub s/ of processor time in each unit cycle for executing aperiodic tasks without missing any periodic-task deadline. The probability of meeting aperiodic-task deadlines is proved to be a monotonic increasing function of R/sub s/. We derive the value of R/sub s/ that maximizes the processor time reservable for the execution of aperiodic tasks without missing any periodic-task deadline. We also show that if the ratio of the computation time to the deadline of each aperiodic task is bounded by R/sub s/, the RB algorithm can meet the deadlines of all periodic and aperiodic tasks. Our analysis and simulation results show that the RB algorithm outperforms all other scheduling algorithms in meeting aperiodic-task deadlines.
ChemInform Abstract: Preparation and Structure of Ba8Ru3.33Ta1.67O18Cl2. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Imaging of Human Lymph Nodes Using Optical Coherence Tomography: Potential for Staging Cancer (2010)

Histologic assessment is the gold standard technique for the identification of metastatic involvement of lymph nodes in malignant disease, but can only be performed ex vivo and often results in the unnecessary excision of healthy lymph nodes, leading to complications such as lymphedema. Optical coherence tomography (OCT) is a high-resolution, near-IR imaging modality capable of visualizing microscopic features within tissue. OCT has the potential to provide in vivo assessment of tissue involvement by cancer. In this morphologic study, we show the capability of OCT to image nodal microarchitecture through an assessment of fresh, unstained ex vivo lymph node samples. Examples include both benign human axillary lymph nodes and nodes containing metastatic breast carcinoma. Through accurate correlation with the histologic gold standard, OCT is shown to enable differentiation of lymph node tissue from surrounding adipose tissue, reveal nodal structures such as germinal centers and intranodal vessels, and show both diffuse and well circumscribed patterns of metastatic node involvement.
The Responsiveness of Embryonic Stem Cells to Alpha and Beta Interferons Provides the Basis of an Inducible Expression System for Analysis of Developmental Control Genes (1993)

Embryonic stem (ES) cells, derived from the inner cell mass of the preimplantation mouse embryo, are used increasingly as an experimental tool for the investigation of early mammalian development. The differentiation of these cells in vitro can be used as an assay for factors that regulate early developmental decisions in the embryo, while the effects of altered gene expression during early embryogenesis can be analyzed in chimeric mice generated from modified ES cells. The experimental versatility of ES cells would be significantly increased by the development of systems which allow precise control of heterologous gene expression. In this paper, we report that ES cells are responsive to alpha and beta interferons (IFNs). This property has been exploited for the development of inducible ES cell expression vectors, using the promoter of the human IFN-inducible gene, 6-16. The properties of these vectors have been analyzed in both transiently and stably transfected ES cells. Expression was minimal or absent in unstimulated ES cells, could be stimulated up to 100-fold by treatment of the cells with IFN, and increased in linear fashion with increasing levels of IFN. High levels of induced expression were maintained for extended periods of time in the continuous presence of the inducing signal or following a 12-h pulse with IFN. Treatment of ES cells with IFN did not affect their growth or differentiation in vitro or compromise their developmental potential. This combination of features makes the 6-16-based expression vectors suitable for the functional analysis of developmental control control genes in ES cells.
The Aspergillus fumigatus Damage Resistance Protein Family Coordinately Regulates Ergosterol Biosynthesis and Azole Susceptibility (2016)

Knowledge of the ergosterol biosynthesis route in fungal pathogens is useful in the design of new antifungal drugs and could aid in the study of antifungal-drug resistance mechanisms. In this study, we demonstrate that three cytochrome b5-like Dap proteins coordinately regulate the azole resistance and ergosterol biosynthesis catalyzed by cytochrome P450 proteins. Our new insights into the Dap regulatory system in fungal pathogens may have broad therapeutic ramifications beyond their usefulness for classic azole antifungals. Moreover, our elucidation of the molecular mechanism of Dap regulation of cytochrome P450 protein functionality through heme-binding activity may extend beyond the Kingdom Fungi with applicability toward Dap protein regulation of mammalian sterol synthesis.