gebhart/patrepeval huggingface dataset:
Computed tomography of the gastrointestinal tract (2022)

Since its initial introduction in the late 1970s, there have been many technical advances in computed tomography (CT) in terms of both scanner hardware and software. The latest generations of multidetector CT (MDCT) scanners have allowed dramatic improvements in both temporal and spatial resolution, making possible studies with minimal respiratory or motion artifacts. This chapter reviews current state-of-the-art CT imaging of the gastrointestinal tract, including the hepatobiliary tree, pancreas, and hollow viscera, as well as ancillary techniques, such as 3D imaging and CT colonography. MDCT is the modality of choice in the detection of distant metastases, most commonly the liver and peritoneum. Although primary neoplasms such as mesothelioma can rarely arise from the peritoneum, the majority of peritoneal tumors reflect involvement of the peritoneum by metastases.
Process Driven Guidance for Complex Surgical Procedures. (2018)

Surgical team processes are known to be complex and error prone. This paper describes an approach that uses a detailed, validated model of a medical process to provide the clinicians who carry out that complex process with offline and online guidance to help reduce errors. Offline guidance is in the form of a hypertext document describing all the ways the process can be carried out. Online guidance is in the form of a context-sensitive and continually updated electronic "checklist" that lists next steps and needed resources, as well as completed steps. In earlier work, we focused on providing such guidance for single-clinician or single-team processes. This paper describes guiding the collaboration of multiple teams of clinicians through complex processes with significant concurrency, complicated exception handling, and precise and timely communication. We illustrate this approach by applying it to a highly complex, high risk subprocess of cardiac surgery.
Performance of immersion lithography for 45-nm-node CMOS and ultra-high density SRAM with 0.25um2 (2007)

Immersion lithography was applied to 45nm node logic and 0.25um<sup>2</sup> ultra-high density SRAM. The predictable enhancement of focus margin and resolution were obtained for all levels which were exposed by immersion tool. In particular, the immersion lithography enabled to apply the attenuating phase shift mask to the gate level. The enough lithography margin for the alternating phase shift mask was also obtained by using not only immersion tool but also dry tool for gate level. The immersion lithography shrunk the minimum hole pitch from 160nm to 140nm. Thus, the design rule for 45nm node became available by using immersion lithography.
Stem Cell Epigenetics (2009)

Epigenetics is the study of heritable changes in gene expression that occur independently of alterations in the primary DNA sequence. Normal development requires a carefully orchestrated epigenetic program on both a global and gene-specific/tissue-specific level. A tightly regulated program of active and repressive histone modifications working in close concert with the methylation of CpG dinucleotides in DNA are responsible for this epigenetic reprogramming, which includes the permanent silencing of genes required for stem/progenitor cell maintenance and the variable regulation of tissue/cell specific activation of genes required for successful differentiation of alternate cell lineages. In this chapter, we will discuss the normal stem/ progenitor cell epigenetic remodeling proteins, including polycomb group (PcG) proteins, and the histone modifications that help modulate gene expression during development. We will highlight the essential role of DNA methylation in gene silencing programs during normal development, including both maternal and paternal imprinting and x-chromosome inactivation, and the permanent silencing of pluripotency-associated genes with terminal differentiation. We will conclude with a more extensive discussion of how the regulatory networks controlling stem cell epigenetics may go awry in cells that give rise to tumors and during tumor progression. The large numbers of epigenetically silenced genes that may be present in any given tumor, and the clustering of silenced genes within single cell pathways, begs the question of whether gene silencing is a series of random events resulting in an enhanced survival of a premalignant clone, or whether silencing is the result of a directed, instructive program for silencing initiation reflective of the cells of origin for tumors. In this regard, the current review stresses the latter hypothesis and the important possibility that the program is linked, at least for silencing of some cancer genes, to the epigenetic control of stem/precursor cell gene expression patterns.
Effect of Design Variables and System-Level Constraints on Heat Pipes Heatsink Performance: Part II - Heat Pipes Staggering and Non-Uniform In-Server Conditions (2019)

In order to investigate the limitations and the theoretical cooling limit of the heat pipe heatsink technology, a parametric study of high-performance heatsinks under different design and in-service constraints was conducted. Although the fluid dynamics and heat transfer of finned heatsinks are well-documented, both experimental and numerical investigations have focused on flowbench-type boundary conditions. Therefore, the impact of surrounding IT equipment, such as upstream electronics, CPU power map, etc., has not be considered for comprehensive design optimization. In this second paper a computational model was developed to investigate the effect of non-uniform features on the heatsink thermal behavior. Of particular interest to this study is to examine the advantages of different heat pipes arrangements while keeping the heat pipes number constant. Four different heat pipes patterns were compared with the original design thermal performance as the associated flow impedance is presented. The impact of non-uniform air flow induced by the upstream IT equipment on the heatsink thermal performance was investigated by dividing the air flow in different number of air streams for different inlet opening percentage. For all analyzed opening areas, the four air streams case presented the best heatsink thermal performance. In order to study the effect of non-uniform heat source over the heatsink thermal behavior, a parametric analysis focused on both power distribution and hotspot orientation with respect the airflow was carried out. Nine symmetrical and three asymmetric fictitious CPU power maps were analyzed. Better heatsink thermal performances were achieved as the heat sources were located away from the center.
Circular Dichroism Thermal Lens Microscope for Sensitive Chiral Analysis on Microchip (2006)

A novel chiral detector, a circular-dichroism thermal lens microscope (CD-TLM), was developed to realize sensitive and selective detection of small volume chiral samples on a microchip. To realize chiral recognition on TLM, an excitation beam was phase-modulated at a frequency of 1.2 kHz, and left-circularly polarized light (LCPL) and right-circularly polarized light (RCPL) were generated. Then, the differential light absorption between LCPL and RCPL, which is the CD effect, was detected as thermal lens signal intensity and phase. As a standard sample, optically active tris(ethylenediamine)cobalt(III) [Co-(en)3]3+I3- aqueous solutions were used for performance evaluations. First, we verified the basic principle for selective chiral analysis by comparing the signals in intensity-modulation and phase-modulation modes of the excitation beam. Also, we found that the g-factor, which is significant for determining enantiomeric excess, agreed well with the value obtained by the CD spectrometer. The limit of detection (LOD) for enantiopure [Co-(en)3]3+I3- was 6.3 x 10(-5) M (1.9 x 10(-7) abs) for (-)-Co(en)3(3+), and the sensitivity in absorbance units was more than 250 times higher than that in a CD spectrophotometer. Finally, we demonstrated enantiomeric excess determination on a microchip. The LOD was 1.7% (8.5 x 10(-7) abs) for (-)-Co(en)3(3+) and at least one order superior to the LOD of a CD spectrometer. The applicability of CD-TLM for sensitive chiral analysis on a microchip was verified, and CD-TLM is expected to be promising for microchip-based chiral synthesis and analysis systems.
TREATMENT OPTIONS FOR THIRD VENTRICULAR COLLOID CYSTS (2008)

We retrospectively reviewed our experience treating third ventricular colloid cysts to compare the efficacy of endoscopic and transcallosal approaches.Between September 1994 and March 2004, 55 patients underwent third ventricular colloid cyst resection. The transcallosal approach was used in 27 patients; the endoscopic approach was used in 28 patients. Age, sex, cyst diameter, and presence of hydrocephalus were similar between the two groups.The operating time and hospital stay were significantly longer in the transcallosal craniotomy group compared with the endoscopic group. Both approaches led to reoperations in three patients. The endoscopic group had two subsequent craniotomies for residual cysts and one repeat endoscopic procedure because of equipment malfunction. The transcallosal craniotomy group had two reoperations for fractured drainage catheters and one operation for epidural hematoma evacuation. The transcallosal craniotomy group had a higher rate of patients requiring a ventriculoperitoneal shunt (five versus two) and a higher infection rate (five versus none). Intermediate follow-up demonstrated more small residual cysts in the endoscopic group than in the transcallosal craniotomy group (seven versus one). Overall neurological outcomes, however, were similar in the two groups.Compared with transcallosal craniotomy, neuroendoscopy is a safe and effective approach for removal of colloid cysts in the third ventricle. The endoscope can be considered a first-line treatment for these lesions, with the understanding that a small number of these patients may need an open craniotomy to remove residual cysts.
Abstract 13185: Monocyte Specific Hydrogen Sulfide Regulates Arteriogenesis in Murine Hind Limb Ischemia (2013)

Background: Monocyte signaling is a dominant and important mediator of arteriogenesis activity and monocyte-signaling responses can be severely impaired during arteriogenesis in various vascular di...
Persistence Criteria for Susceptibility Genes for Schizophrenia: a Discussion from an Evolutionary Viewpoint (2009)

If we assume the nuclear DNA model for schizophrenia, it should have many susceptibility genes of exceptionally high mutation rates; alternatively, it should have many disease-associated resistance genes of standard mutation rates on different chromosomes. On the other hand, the epidemiological data show that pathogenic genes, if located in the mitochondrial DNA, could persist through sex-related mechanisms.
Bone Marrow Therapy for Myocardial Infarction (2011)

The results of the latetime study, 1 reported by Traverse and colleagues in this issue of JAMA, appear 1 decade after the publication of the landmark study by Orlic et al. 2 The authors conducted a rigorous clinical trial to test the hypothesis that intracoronary infusion of autologous bone marrow mononuclear cells (BMCs) in patients with myocardial infarction (MI) would improve left ventricular function.The rationale for using whole bone marrow in this setting derives from numerous sets of experimental studies showing that bone marrow contains cellular constituents that have cardiac reparative ability. 2,3The authors found that among 87 patients with MI and left ventricular dysfunction following reperfusion with percutaneous coronary intervention, compared with placebo intracoronary infusion, intracoronary infusion of BMCs 2 to 3 weeks after percutaneous coronary intervention did not improve global or regional ventricular function at 6 months.Given its rigorous design with placebo control, blinding, and sophisticated magnetic resonance imaging (MRI), the LateTIME trial results are compelling, arguing against the value of intracoronary bone marrow infusion administration 2 to 3 weeks following acute MI.The results of the LateTIME trial are in contrast with several other rigorous clinical trials, notably the Reinfusion of Enriched Progenitor Cell and Infarct Remodeling in Acute Myocardial Infarction (REPAIR-AMI) published in 2006, 4 which showed a statistically significant increase in ejection fraction (EF) in response to intracoronary bone marrow given within 3 to 7 days of MI.In that study, the authors found that the benefit increased among patients treated toward the end of the 7-day time frame, with an enhanced effect in the subgroup of patients with EFs less than the median of 48.9%.The results of a meta-analysis 5 substantiated the finding that intracoronary BMCs are associated with an improvement in EF by approximately 3% to 4%.Additionally, a potentially important analysis from the REPAIR-AMI data suggests that intracoronary BMCs may have clinical benefits that exceed those predicted by the increase in EF. 6 Importantly, 2 ongoing current trials-TIME 7 and BAMI (Bone marrow-derived mononuclear cells [BM-MNC] on all-cause mortality in Acute Myocardial Infarction)-will offer important information.The TIME study, 7 conducted by the same investigators as the LateTIME study, will compare the efficacy of bone marrow therapy at 3 vs 7 days, and the
Challenges on the frontier of intracoronary imaging: atherosclerotic plaque macrophage measurement by optical coherence tomography (2010)

Cellularity of the fibrous caps of coronary atheromas, manifested by the infiltration of macrophages (average size, 20 to 30 microm), is thought to weaken the structural integrity of the cap and predispose plaques to rupture. Therefore, an imaging technology capable of identifying macrophages within fibroatheroma caps in patients could provide valuable information for assessing plaque rupture risk. Recently, intravascular optical coherence tomography (OCT), a high-resolution coronary imaging modality, with an axial resolution of approximately 10 microm, has been introduced into the clinical setting. OCT images of the microstructure of the coronary artery wall enable accurate plaque-type characterization, supported by histopathological comparison data. Because of its high resolution, OCT may also be used to identify macrophages in vivo. In this paper we review recent developments in OCT for measuring macrophages in atherosclerotic plaques.
Characterization of Fourier components in type I infrared ultrafast laser induced fiber Bragg gratings (2007)

Type I infrared ultrafast laser induced fiber Bragg gratings have been shown to exhibit higher-order resonances related to the Fourier components possessed by their nonsinusoidal index change profile. Using successive higher-order phase masks, we determine the Fourier components of type I-IR gratings in both hydrogen-loaded and unloaded fiber. Knowledge of the relative dc and ac components of a fiber Bragg grating is required for tailoring its spectral response.
Micro- and nano-electro mechanical (MEMS and NEMS)-based technologies for implanted biomedical devices (2008)

The next generation of implantable biomedical devices based on micro- and nano-electro-mechanical systems (MEMS and NEMS) technology is presented for diagnostics and treatment of chronic and non-chronic illnesses. These passive and active implantable devices allow for early diagnostics as well as timely and precisely controlled therapeutic drug delivery. The implantable devices are also applicable to a number of medical applications, including the next generation of early cancer diagnostics and treatments.
Flow Properties of Selected Pharmaceutical Powders from a Vibrating Spatula (1994)

Abstract Studies have been performed to characterize the flow of certain powders of pharmaceutical interest from a vibrating spatula. Lactose, cromolyn sodium, sodium chloride and charcoal powders were prepared by milling or sieving. Jet milling yielded micronized powder (1–10 μm), which was recovered from the product jar or metal cyclone. Particles in the larger size ranges were prepared by sieving. Photomicrograph images of the products were obtained by scanning electron microscopy. All of the powders were subjected to flow studies from vibrating beds to a top loading pan balance. Cumulative mass versus time, flow profiles were plotted. Bulk flow properties, as reflected in mass flow rates (M i ), were assessed. Irregular flow patterns were obtained for lactose, cromolyn sodium and charcoal, whereas sodium chloride was free flowing. The lengths of the lines depicting cumulative mass versus time, for samples of each material, were estimated using the inswing structured walk technique. Stride lengths (γ) of 1–100 mm were employed. Fractal dimensions were obtained from graphs of the logarithm of the cumulative mass versus time line length plotted against the logarithm of the stride length. Thus, flow irregularities were indicated by fractal dimensions (δ). In all of the powders studied, mass flow rates increased as the particle size increased. Sodium chloride did not exhibit fractal behavior (δ ≤ 1.007), as there were no flow irregularities. Lactose, cromolyn sodium and charcoal did not appear to exhibit fractal behavior (δ ≤ 1.010) at large stride lengths (γ = 15–100 mm). At small stride lengths (γ = 1–10 mm) these materials did exhibit fractal behavior (δ equals; 1.029–1.059) indicative of flow irregularity. This method may be used to numerically quantify uniformity of flow from a vibrating spatula, and would be useful in a number of industrial processes.
Lookout for Zombies: Mitigating Flush+Reload Attack on Shared Caches by Monitoring Invalidated Lines (2019)

OS-based page sharing is a commonly used optimization in modern systems to reduce memory footprint. Unfortunately, such sharing can cause Flush+Reload cache attacks, whereby a spy periodically flushes a cache line of shared data (using the clflush instruction) and reloads it to infer the access patterns of a victim application. Current proposals to mitigate Flush+Reload attacks are impractical as they either disable page sharing, or require application rewrite, or require OS support, or incur ISA changes. Ideally, we want to tolerate attacks without requiring any OS or ISA support and while incurring negligible performance and storage overheads. This paper makes the key observation that when a cache line is invalidated due to a Flush-Caused Invalidation (FCI), the tag and data of the invalidated line are still resident in the cache and can be used for detecting Flush-based attacks. We call lines invalidated due to FCI as Zombie lines. Our design explicitly marks such lines as Zombies, preserves the Zombie lines in the cache, and uses the hits and misses to Zombie lines to tolerate the attacks. We propose Zombie-Based Mitigation (ZBM), a simple hardware-based design that successfully guards against attacks by simply treating hits on Zombie-lines as misses to avoid any timing leaks to the attacker. We analyze the robustness of ZBM using three spy programs: attacking AES T-Tables, attacking RSA Square-and-Multiply, and Function Watcher (FW), and show that ZBM successfully defends against these attacks. Our solution requires negligible storage (4-bits per cache line), retains OS-based page sharing, requires no OS/ISA changes, and does not incur slowdown for benign applications.
Supplementary Data from Intertumoral Heterogeneity of CD3<sup>+</sup> and CD8<sup>+</sup> T-Cell Densities in the Microenvironment of DNA Mismatch-Repair–Deficient Colon Cancers: Implications for Prognosis (2023)

&lt;p&gt;Figure S1 Study flow of N0147 patient tumor samples Figure S2 Heterogeneity of lymphocytic infiltrate between patients in mismatch repair deficient (dMMR) and proficient (pMMR) tumors. The distribution of T-cell densities (score 0-100) are shown as follows: (a) CD3+ in the core of the tumor, (b) CD8+ at the invasive margin, (c) CD8+ in the core of the tumor. For each T-cell subtype, density of tumor infiltration was higher in dMMR vs pMMR tumors (each p &lt;.001).&lt;/p&gt;
Impact of Gas–Condensate Composition and Interfacial Tension on Oil-Repellency Strength of Wettability Modifiers (2014)

Productivity of gas–condensate wells can significantly be declined as the condensate bank evolves around the wellbore. Wettability alteration of formation minerals from strongly liquid-wet to intermediate gas-wet conditions using liquid-repellent fluorinated chemicals has shown promising results to mitigate such liquid-blockage issues. This paper, for the first time, presents the results of unique contact angle measurements conducted on the treated carbonate substrates using synthetic gas–condensate fluids. The impact of hydrocarbon composition and interfacial tension (IFT) on the condensate wetting tendency was investigated using various binary and multi-component mixtures at ambient temperature. A high-pressure high-temperature (HPHT) drop shape analysis setup was customized to perform the static contact angle tests. The generality of the new findings from these measurements was also confirmed using dynamic unsteady-state flow tests. The results demonstrated that the wetting tendency of the condensate is significantly decreased as IFT increases and/or the hydrocarbon composition becomes heavier. The C1–nC4 condensate drop, for instance, completely wetted out the treated surface at both low- and high-IFT limits of 1 and 10 mN/m, whereas the C1–nC10 sample resulted in contact angles of 30° and 65° at similar IFT conditions, respectively. The oil-repellency strength of the fluorochemical was also evaluated at high temperatures of 50 and 100 °C with promising results. In this paper, the initial investigations on the impact of surface roughness on the solid surface wettability was carried out, demonstrating the positive impact of surface roughness on increasing the desired level of oil repellency achieved after the wettability alteration. The new findings from this work provide important guidelines in design and application of wettability modifiers for gas–condensate reservoirs.
Flexible Consistency for Wide Area Peer Replication (2005)

The lack of a flexible consistency management solution hinders P2P implementation of applications involving updates, such as read-write file sharing, directory services, online auctions and wide area collaboration. Managing mutable shared data in a P2P setting requires a consistency solution that can operate efficiently over variable-quality failure-prone networks, support pervasive replication for scaling, and give peers autonomy to tune consistency to their sharing needs and resource constraints. Existing solutions lack one or more of these features. In this paper, we describe a new consistency model for P2P sharing of mutable data called composable consistency, and outline its implementation in a wide area middleware file service called Swarm¹. Composable consistency lets applications compose consistency semantics appropriate for their sharing needs by combining a small set of primitive options. Swarm implements these options efficiently to support scalable, pervasive, failure-resilient, wide-area replication behind a simple yet flexible interface. We present two applications to demonstrate the expressive power and effectiveness of composable consistency: a wide area file system that outperforms Coda in providing close-to-open consistency overWANs, and a replicated BerkeleyDB database that reaps order-of-magnitude performance gains by relaxing consistency for queries and updates.