gebhart/patrepeval huggingface dataset:
CFD Analysis of the Frame Invariance of the Melt Temperature Rise in a Single-screw Extruder (2013)

Abstract In analytical analyses for single-screw extruders the simplified approach of rotating the barrel and keeping the screw fixed is often used instead of rotating the screw and fixing the barrel. Although the flow field is independent of the reference frame, as has already been shown to a satisfactory degree (Rauwendaal et al., 1997), the question of the dependence of the melt temperature rise on the reference frame is still being challenged, e.g. Campbell et al. (2001, 2008). In this work we develop a finite-volume CFD code allowing for the three-dimensional simulation of the flow and temperature rise in both reference frames. The question of frame invariance is addressed by simulating the flow of a Newtonian-like polycarbonate both in a two-dimensional cross-section of a single-screw extruder and in a three-dimensional model with two full turns of the screw. Our results show that the kinematics and the melt temperature rise are equal for screw- and barrel-rotation and thus independent of the reference frame. Furthermore, the presence of a clearance flow has a negligible influence on the temperature rise.
Quantum cascade laser-based dual-comb spectroscopy in the mid-infrared (2018)

We demonstrate sub-millisecond response time dual-comb spectroscopy using quantum cascade lasers by measurements of Bromomethane and Freon 134a around 7.7 µm. The system achieves a noise-equivalent absorption of &lt;1×10−3 Hz−1/2 and an optical bandwidth of ~25 cm−1.
Piezo-Hall effect in single crystal p-type 3C–SiC(100) thin film grown by low pressure chemical vapor deposition (2016)

This article reports the first results on piezo-Hall effect in single crystal p-type 3C–SiC(100) Hall devices.
Correlation of Zeno (<i>Z</i> = 1) Line for Supercritical Fluids with Vapor‐Liquid Rectilinear Diameters (1990)

Abstract For a wide range of substances, extending well beyond the regime of corresponding states behavior, the contour in the temperature‐density plane along which the compressibility factor Z = P/ρkT is the same as for an ideal gas is nearly linear. This Z = 1 contour, termed the Zeno line, begins deep in the liquid region and ascends as the density decreases to the Boyle point of the supercritical fluid, specified by the temperature T B for which ( dZ/dρ ) T = 0 as ρ → 0; equivalently, at T B the second virial coefficient vanishes. The slope of the Z = 1 line is — B 3 /( dB 2 / dT ), in terms of the third virial coefficient and the derivative of the second, evaluated at T B . Previous work has examined the Zeno line as a means to extend corresponding states and to enhance other practical approximations. Here we call attention to another striking aspect, a strong correlation with the line of rectilinear diameters defined by the average of the subcritical vapor and liquid densities. This correlation is obeyed well by empirical data for many substances and computer simulations for a Lennard‐Jones potential; the ratios of the intercepts and slopes for the Zeno and rectilinear diameter lines are remarkably close to those predicted by the van der Waals equation, 8/9 and 16/9, respectively. Properties of the slightly imperfect fluid far above the critical point thus implicitly determine the diameter of the vapor‐liquid coexistence curve below the critical point.
Interpretable Bias Mitigation for Textual Data: Reducing Genderization in Patient Notes While Maintaining Classification Performance (2022)

Medical systems in general, and patient treatment decisions and outcomes in particular, can be affected by bias based on gender and other demographic elements. As language models are increasingly applied to medicine, there is a growing interest in building algorithmic fairness into processes impacting patient care. Much of the work addressing this question has focused on biases encoded in language models—statistical estimates of the relationships between concepts derived from distant reading of corpora. Building on this work, we investigate how differences in gender-specific word frequency distributions and language models interact with regards to bias. We identify and remove gendered language from two clinical-note datasets and describe a new debiasing procedure using BERT-based gender classifiers. We show minimal degradation in health condition classification tasks for low- to medium-levels of dataset bias removal via data augmentation. Finally, we compare the bias semantically encoded in the language models with the bias empirically observed in health records. This work outlines an interpretable approach for using data augmentation to identify and reduce biases in natural language processing pipelines.
The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region (2017)

Small isoprenoid diphosphates, such as (<i>E</i>)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), are ligands of the internal domain of BTN3A1. Ligand binding in target cells promotes activation of Vγ9Vδ2 T cells. We demonstrate by small-angle X-ray scattering (SAXS) that HMBPP binding to the internal domain of BTN3A1 induces a conformational change in the position of the B30.2 domain relative to the juxtamembrane (JM) region. To better understand the molecular details of this conformational rearrangement, NMR spectroscopy was used to discover that the JM region interacts with HMBPP, specifically at the diphosphate. The spectral location of the affected amide peaks, partial NMR assignments, and JM mutants (ST<sup>296</sup>AA or T<sup>304</sup>A) investigated, confirm that the backbone amide of at least one Thr (Thr<sup>304</sup>), adjacent to conserved Ser, comes close to the HMBPP diphosphate, whereas double mutation of nonconserved residues (Ser/Thr<sup>296/297</sup>) may perturb the local fold. Cellular mutation of either of the identified Thr residues reduces the activation of Vγ9Vδ2 T cells by HMBPP, zoledronate, and POM<sub>2</sub>-C-HMBP, but not by a partial agonist BTN3 antibody. Taken together, our results show that ligand binding to BTN3A1 induces a conformational change within the intracellular domain that involves the JM region and is required for full activation.-Nguyen, K., Li, J., Puthenveetil, R., Lin, X., Poe, M. M., Hsiao, C.-H. C., Vinogradova, O., Wiemer, A. J. The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region.
Pioglitazone Reduces Vascular Lipid Accumulation in Angiotensin II-Induced Hypertensive Rat (2015)

Pioglitazone treatment suppressed excess lipid accumulation and superoxide production in the aorta in an angiotensin II-induced rat model of hypertension.
Neural inhibition of inflammation: the cholinergic anti-inflammatory pathway (2003)

The innate immune system is activated by infection and injury to release pro-inflammatory cytokines, which activate macrophages and neutrophils and modulate specific cellular responses. The magnitude of the cytokine response is critical, because a deficient response may result in secondary infections, while an excessive response may be more injurious than the original insult. We recently described a neural pathway, termed the `cholinergic anti-inflammatory pathway', that reflexively monitors and adjusts the inflammatory response by inhibiting pro-inflammatory cytokine synthesis. Efferent signals in the vagus nerve provide a direct mechanism for neural regulation of the immune response that is rapid, localized, and integrated. Vagus nerve stimulation inhibits the release of TNF, HMGB1, and other cytokines, and protects against endotoxemia and ischemia-reperfusion injury. This newly identified physiological mechanism of maintaining immunological homeostasis suggests that novel therapeutics may effectively modulate inflammatory responses by activating the cholinergic anti-inflammatory pathway.
The Lymphatics: On the Route to Cancer Metastasis (2011)

The blood vascular and lymphatic systems are necessary for the flux of gases, liquids, nutrients, signaling molecules, and cells among tissues and organs. These two highly branched, treelike networks are interconnected through the largest lymphatic vessel, the thoracic duct, which drains lymph, the protein-rich interstitial fluid, into the blood circulation. Both networks contribute to homeostasis of a healthy individual, and their malformation or dysfunction contributes to the pathogenesis of many diseases, such as cancer [1].
Health planning in Pakistan: a case study (1997)

Health planning is an essential function of the state. For it to be successful, a number of conditions need to be satisfied. In particular it needs to be flexible, participative and integrated with other decision processes. Despite some strengths, the health planning system in Pakistan has generally failed to provide the framework to allow such an approach. Links between strategic and operational planning have been weak; decision-making has been very centralized; there has been a lack of functional clarity; the respective roles of bureaucrats and politicians have been unclear; and, links between capital and recurrent budgets and between planning and implementation have been weak. As a result, there is a number of imbalances in the allocation of resources. The introduction of a revised health planning system for Pakistan is discussed. The constraints on such a system and an initial assessment of its success are presented.
Targeting Cancer Stem Cells: Promises and Challenges (2015)

Recent discoveries have provided the compelling evidence that stem cell populations within each individual tumor are key contributors of therapy failure regardless of whether these populations are transient or stable. Thus, it is becoming increasingly clear that efficient tumor treatment requires eradication of the entire CSC population. The potential role of CSCs in tumor initiation and relapse has motivated an investigation of the CSCspecific treatments. However, development of the therapeutic strategies targeting CSCs might be challenged by a high diversity and plasticity of CSC features. Moreover, taking in account that an origin of CSC remains controversial and accumulating experimental evidence suggests a possibility of tumor cell reprogramming, efficient anti-cancer treatment should eradicate both CSCs and tumor bulk as well as prevent tumor dedifferentiation. In this article we discuss new insights into the stem cell concept of tumor development, review the treatment strategies eradicating CSCs that have been evaluated in preclinical and clinical studies and summarize the strategies to identify new CSC-targeted therapy.
Data from Multimodality Treatment of Desmoplastic Small Round Cell Tumor: Chemotherapy and Complete Cytoreductive Surgery Improve Patient Survival (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Desmoplastic small round cell tumor (DSRCT), which harbors EWSR1-WT1 t(11;22)(p13:q12) chromosomal translocation, is an aggressive malignancy that typically presents as intra-abdominal sarcomatosis in young males. Given its rarity, optimal treatment has not been defined.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We conducted a retrospective study of 187 patients with DSRCT treated at MD Anderson Cancer Center over 2 decades. Univariate and multivariate regression analyses were performed. We determined whether chemotherapy, complete cytoreductive surgery (CCS), hyperthermic intraperitoneal cisplatin (HIPEC), and/or whole abdominal radiation (WART) improve overall survival (OS) in patients with DSRCT. Critically, because our institutional practice limits HIPEC and WART to patients with less extensive, potentially resectable disease that had benefited from neoadjuvant chemotherapy, a time-variant analysis was performed to evaluate those adjunct treatment modalities.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The pre-2003 5-year OS rate of 5% has substantially improved to 25% with the advent of newer chemotherapies and better surgical and radiotherapy techniques (HR, 0.47; 95% CI, 0.29–0.75). Chemotherapy response (log rank &lt;i&gt;P&lt;/i&gt; = 0.004) and CCS (log rank &lt;i&gt;P&lt;/i&gt; &lt; 0.0001) were associated with improved survival. Although WART and HIPEC lacked statistical significance, our study was not powered to detect their potential impact upon OS.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Improved 3- and 5-year OS were observed following multidisciplinary treatment that includes Ewing sarcoma (ES)-based chemotherapy and complete tumor cytoreductive surgery, but few if any patients are cured. Prospective randomized studies will be required to prove whether HIPEC or WART are important. In the meantime, chemotherapy and CCS remain the cornerstone of treatment and provide a solid foundation to evaluate new biologically targeted therapies. &lt;i&gt;Clin Cancer Res; 24(19); 4865–73. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
P301 Non-familial small bowel carcinomas in Crohn's disease: clinico-pathological, molecular and prognostic features (2017)

Background: An increased risk for small bowel carcinoma (SBC) has been reported in Crohn's disease (CrD). We aimed to explore clinical, histopathologic, molecular and prognostic features of CrD-associated SBC (CrD-SBC) in comparison to both coeliac disease (CD)-associated SBC (CD-SBC) and sporadic SBC (spo-SBC). Methods: Seventy-six patients, who underwent surgical resection for non-familial SBC (25 CrD-SBC26, CD-SBC and 25 spo-SBC), were retrospectively recorded to investigate survival together with histological and molecular features detected by immunohistochemistry, multiplex PCR and sequencing. Results: CD-SBC showed a significantly (p=0.004) better sex-, age- and stage-adjusted overall and cancer-specific survival in comparison to CrD-SBC, while no significant difference was found between spo-SBC and either CD-SBC or CrD-SBC. CD-SBC exhibited a significantly (p=0.001) higher rate of microsatellite instability (MSI, 65%) compared to both CrD-SBC (16%) and Spo-SBC (16%). The median number of tumor-infiltrating lymphocytes (TIL) correlated with MSI status and was significantly higher in CD-SBC than in both CrD-SBC (p<0.001) and spo-SBC (p=0.002). Among CD-SBC, MSI allowed to separate two subgroups with different outcome, stage and TP53 mutation rate. MSI was the result of MLH1 methylation in all cases (with the exception of one case of CrD-SBC). No BRAF mutation was observed in any SBC. Mutations in KRAS, NRAS, and PIK3CA were detected in 30%, 4% and 13% of cases, respectively. HER2 gene amplification was identified in two CD-SBC, two CrD-SBC and one spo-SBC. Conclusions: In comparison to CrD-SBC, CD-SBC harbor much more frequently MSI and show a more favorable prognosis, likely related to their high density of TILs, which have independent prognostic value in SBC. MSI status, KRAS/NRAS mutations and HER2 amplifications might contribute to stratify patients for targeted anti-cancer therapy.
Roles of Arabidopsis <i>AtREV1</i> and <i>AtREV7</i> in Translesion Synthesis (2005)

Plants have mechanisms for repairing and tolerating detrimental effects by various DNA damaging agents. A tolerance pathway that has been predicted to be present in higher plants is translesion synthesis (TLS), which is catalyzed by polymerases. In Arabidopsis (Arabidopsis thaliana), however, the only gene known to be involved in TLS is the Arabidopsis homolog of REV3, AtREV3, which is a putative catalytic subunit of Arabidopsis DNA polymerase zeta. A disrupted mutant of AtREV3, rev3, was previously found to be highly sensitive to ultraviolet-B (UV-B) and various DNA damaging agents. REV1 and REV7 are thought to be components of translesion synthesis in plants. In this study, we identified the Arabidopsis homologs of REV1 and REV7 (AtREV1 and AtREV7). Several mutants carrying disrupted AtREV1 and AtREV7 genes were isolated from Arabidopsis T-DNA-inserted lines. An AtREV1-disrupted mutant, rev1, was found to be moderately sensitive to UV-B and DNA cross-linkers. A rev1rev3 double mutant, like rev3, showed high sensitivity to UV-B, gamma-rays, and DNA cross-linkers. An AtREV7-disrupted mutant, rev7, was possibly sensitive to cis-diamminedichloroplatinum(II), a kind of DNA cross-linker, but it was not sensitive to acute UV-B and gamma-ray irradiation. On the other hand, the aerial growth of rev7, like the aerial growth of rev1 and rev3, was inhibited by long-term UV-B. These results suggest that a TLS mechanism exists in a higher plant and show that AtREV1 and AtREV7 have important roles in tolerating exposure to DNA-damaging agents.
The Role of Stressor Intensity in Influencing the Course of Heart Disease in Cardiomyopathic Hamsters (1996)

Our earlier work showed that stress had progressively more serious consequences in a hamster model of congestive heart failure as the magnitude of heart failure worsened. Based on that study, we hypothesized that the intensity of the stressor used might play an important part in determining this outcome as well as in influencing coronary reactivity to arginine vasopressin (AVP). Cardiomyopathic (2.5, 6.5, and 10 months) hamsters (CMHs) were stressed with a 2-hr period of supine immobilization for five consecutive days. Stressor intensity was increased by exposing the hamsters to progressively longer periods at 4 degrees C: the low stress group was never put in the cold; the moderate stress group was exposed to cold for 1 hr, and the high stress group for 2 hr. CMHs were anesthetized and sacrificed 5 days after stress, and their hearts were perfused using a modified Langendorff system. Maximum +/- dP/dt, developed pressure, ventricular relaxation time, (T), and coronary vascular resistance (CVR) were recorded, and CVR was also measured following coronary infusion of AVP. Stressor intensity had no effect on cardiac mechanics in 2.5-month CMHs. In 6.5-month CMHs, only the high-intensity stressor impaired ventricular mechanics (decreased maximum +/- dP/dt and developed pressure, increased T; P < 0.05), while low and moderate stress produced no effects. In 10-month CMHs, stress at all intensities exacerbated ventricular dysfunction (decreased maximum +/- dP/dt and developed pressure; P < 0.05). These results support our first hypothesis that stressor intensity interacts multiplicatively with severity of the underlying disease to influence the course of heart failure. However, our second hypothesis was not supported, because stress-regardless of intensity-affected reactivity of the coronary vasculature to AVP only in 2.5-month CMHs. A further test of the relation of stressor intensity and coronary vascular reactivity requires study of additional groups of CMHs during the period of their disease characterized by coronary vasospasm.
Chemical synthesis and purification of proteins: a methodology (1996)

Classical stepwise solid‐phase peptide synthesis (SPPS) has been used successfully for the synthesis of proteins up to 150 residues in length, although usually with poor yields and homogeneity. The major limitation has been the inability to separate chromatographically similar deletion and truncated impurities from the target sequence. We have developed a highly effective protocol for stepwise SPPS and‘one‐step’purification of small proteins. To demonstrate the effectiveness of the methodology we synthesised the 101 residue chaperonin 10 protein from Rattus norvegicus (Rat Cpnl0) using three different chemical protocols. Highly homogeneous Rat Cpnl0 was obtained using an optimised synthetic strategy and one‐step purification procedure (method C), involving (i) HBTU/HOBt activation, (ii) N ‐(2‐chlorobenzyloxy‐carbonyloxy)succinimide as capping agent and (iii) the incorporation of a reversible Fmoc‐based chromatographic probe, derivatised with a lipophilic group for fast one‐step RP purification, to give an overall yield of 9.6%. Analysis by ESI‐MS indicated that the product was virtually free of deletion impurities, while RP‐HPLC under four different conditions and CZE indicated that the protein was 100 and 84% pure, respectively. The spontaneous folding of Rat Cpnl0 into its biologically active form was found to correlate well with the degree of purity as assessed by chromatography, ESI‐MS and sequencing, since 29 (A), 55 (B) and 81% (C) of correctly folded heptameric structure was obtained. The degree of homogeneity was also reflected in the ability of purified Rat Cpnl0 to facilitate the refolding of yeast enolase. © Munksgaard 1996.
Infrared Investigation of Dynamic Behavior of Brønsted Acid Sites on Zeolites at High Temperatures (2017)

Temperature-dependent behavior of acidic OH groups on zeolites was observed by infrared (IR) spectroscopy. While the IR band of acidic OH groups appeared the same in frequency and intensity below 300 K, gradual shifts in the peak-top position to lower frequencies and decreases in integrated intensity were recognized when samples were heated at higher temperatures. These changes were completely reversible and only dependent on the temperature. Based on the assumption that there is an equilibrium between undissociated and dissociated states of OH groups, a model is proposed in which the intensity decrease is attributed to the dissociation of OH groups to form IR inactive species at high temperatures. The enthalpy difference between the two states was estimated using the van’t Hoff equation, leading to two different values in two temperature ranges (about 398–548 and 573–773 K) for zeolites with various topologies (MFI, MOR, and CHA). Based on the presence of two different types of enthalpy values, different mechanisms were proposed for these two situations. Liberated protons may move across four lattice oxygen atoms around the Al site at lower temperatures (around 550 K or below). At high temperatures, the protons may move in wider regions over the framework. DFT calculations show that the frequency of the OH band varies depending on which of the four different oxygen atoms around the Al site acts as the proton acceptor. The experimentally observed peak-top shift to the lower frequency side is explained by assuming that the population of protons changed with temperature such that more protons reside at low-frequency sites at higher temperatures. This process is interpreted as localized hopping or limited delocalization. At the higher temperature range (573–773 K), the enthalpy difference was independent of the Al amount but was only dependent on the zeolite topology. This supports the free hopping of protons over the framework. The enthalpy difference at higher temperatures increased in the order CHA < MFI < MOR, indicating that a zeolite with smaller pores tends to generate more protons at the same temperature. In other words, zeolites with small pores function as stronger acid catalysts for reactions at high temperatures. This proposition was supported by experimental results of a monomolecular reaction taking place at a single site, that is, H/D isotope exchange between acidic OD groups and CH4.
Controlled, Bio‐inspired Self‐Assembly of Cellulose‐Based Chiral Reflectors (2014)

The self-assembly process of photonic structures made of cellulose nanocrystals is studied in detail by locally monitoring and controlling water evaporation. Three different stages during the evaporation process are identified. Spectroscopy quantifies the amount of disorder in the fabricated samples. Control of this process enables the selection of a range of different colors starting from the same suspension, providing a facile, sustainable route for the manufacture of structural color.
KINETIC PATHWAY IN STRANSKI-KRASTANOV GROWTH OF Ge ON Si(001) (1990)

Scanning tunneling microscopy studies of the kinetic processes involved in the two-dimensional (2D) to three-dimensional (3D) transition in Stranski-Krastanov growth of Ge on Si(001) reveal a novel type of 3D cluster that serves as the kinetic pathway for this transition.