gebhart/patrepeval huggingface dataset:
When Did the Human Population Size Start Increasing? (2000)

We analyze the frequency spectra of all available human nuclear sequence data sets by using a model of constant population size followed by exponential growth. Parameters of growth (more extreme than or) comparable to what has been suggested from mtDNA data can be rejected for 6 out of the 10 largest data sets. When the data are separated into African and non-African samples, a constant size no-growth model can be rejected for 4 out of 8 non-African samples. Long-term growth (i.e., starting 50-100 kya) can be rejected for 2 out of 8 African samples and 5 out of 8 non-African ones. Under more complex demographic models, including a bottleneck or population subdivision, more of the data are compatible with long-term growth. One problem with the data used here is that a subset of loci may reflect the action of natural selection as well as of demography. It remains possible that the correct demographic model is one of constant population size followed by long-term growth but that at several loci the demographic signature has been obscured by balancing or diversifying selection. However, it is not clear that the data at these loci are consistent with a simple model of balancing selection; more complicated selective alternatives cannot be tested unless they are made explicit. An alternative explanation is that population size growth is more recent (e.g., upper Paleolithic) and that some of the loci have experienced recent directional selection. Given the available data, the latter hypothesis seems more likely.
Plasma leptin and colorectal cancer risk: A prospective study in Northern Sweden (2003)

Obesity is associated with an increased risk of colorectal cancer. Circulating levels of leptin are high in obesity and strongly correlated to levels of insulin. Leptin stimulates growth of colon cancer cells. In a nested case-control study, we measured leptin levels in prediagnostic plasma from 75 men and 93 women who were diagnosed with colorectal cancer mean time 3.4 years (SD 2.4) after recruitment and among 327 control subjects. Logistic regression analyses showed increases in colorectal cancer risk in men with increasing levels of leptin, odds ratios (OR) were 1.00 (ref), 0.85 (95% C.I.=0.33-2.23), 1.04 (0.43-2.53), and 2.15 (0.89-5.22), (pfor trend=0.08). There was a distinct threshold between the third and fourth quartile of leptin, and the odds ratio for top quartile vs. three bottom quartiles was 2.28 (1.09-4.76). Adjustment for body mass index and insulin did not affect risk estimates. In separate analysis, odds ratio for top vs. bottom tertile of colon cancer was 1.96 (95% C.I.=0.72-5.29), whereas no increase was seen for rectal cancer. In women, no association between leptin and risk was seen. These data support the hypothesis that leptin is a risk marker for colorectal cancer in men, but not in women.
Absolute positioning by multi-wavelength interferometry referenced to the frequency comb of a femtosecond laser (2015)

A multi-wavelength interferometer utilizing the frequency comb of a femtosecond laser as the wavelength ruler is tested for its capability of ultra-precision positioning for machine axis control. The interferometer uses four different wavelengths phase-locked to the frequency comb and then determines the absolute position through a multi-channel scheme of detecting interference phases in parallel so as to enable fast, precise and stable measurements continuously over a few meters of axis-travel. Test results show that the proposed interferometer proves itself as a potential candidate of absolute-type position transducer needed for next-generation ultra-precision machine axis control, demonstrating linear errors of less than 61.9 nm in peak-to-valley over a 1-meter travel with an update rate of 100 Hz when compared to an incremental-type He-Ne laser interferometer.
Lactobacilli activate human dendritic cells that skew T cells toward T helper 1 polarization (2005)

Professional antigen-presenting dendritic cells (DCs) are critical in regulating T cell immune responses at both systemic and mucosal sites. Many Lactobacillus species are normal members of the human gut microflora and most are regarded as safe when administered as probiotics. Because DCs can naturally or therapeutically encounter lactobacilli, we investigated the effects of several well defined strains, representing three species of Lactobacillus on human myeloid DCs (MDCs) and found that they modulated the phenotype and functions of human MDCs. Lactobacillus-exposed MDCs up-regulated HLA-DR, CD83, CD40, CD80, and CD86 and secreted high levels of IL-12 and IL-18, but not IL-10. IL-12 was sustained in MDCs exposed to all three Lactobacillus species in the presence of LPS from Escherichia coli, whereas LPS-induced IL-10 was greatly inhibited. MDCs activated with lactobacilli clearly skewed CD4(+) and CD8(+) T cells to T helper 1 and Tc1 polarization, as evidenced by secretion of IFN-gamma, but not IL-4 or IL-13. These results emphasize a potentially important role for lactobacilli in modulating immunological functions of DCs and suggest that certain strains could be particularly advantageous as vaccine adjuvants, by promoting DCs to regulate T cell responses toward T helper 1 and Tc1 pathways.
Difluoromethylornithine chemoprevention of epidermal carcinogenesis in K14-HPV16 transgenic mice. (1999)

To be informative for chemoprevention, animal models must both closely emulate human disease and possess surrogate endpoint biomarkers that facilitate rapid drug screening. This study elucidated site-specific histopathological and biochemical surrogate endpoint biomarkers of spontaneous epidermal carcinogenesis in K14-HPV16 transgenic mice and demonstrated that the incidence and severity of these markers were decreased by the ornithine decarboxylase (ODC) inhibitor difluoromethylornithine (DFMO). The cumulative incidence of visible epidermal cancers in 127 untreated transgenic mice was 42% by 52 weeks of age, most frequently affecting the chest as flat lesions in association with chronic ulcers, or in the ear as protuberant masses. Microscopic malignancies were detected in 39% of 32-week-old transgenic mice and were found to emerge from precursor lesions that were of two distinct types: dysplastic sessile ear papillomas and hyperproliferative follicular/interfollicular chest dysplasias. ODC activity and tissue polyamine contents were differentially elevated in ear and chest skin during carcinogenesis, such that there was a marked elevation of both parameters of polyamine metabolism as early as 4 weeks of age in the ear, whereas in the chest, polyamine metabolism was increased significantly only in the late stages of neoplastic progression and in epidermal cancers. Administration of 1.0% DFMO in the drinking water from 4 to 32 weeks of age prevented both visible and microscopic malignancies and significantly decreased the incidence of chest and ear precursor lesions. ODC activity and tissue putrescine content were markedly diminished by DFMO chemoprevention in ear skin, whereas there was a more modest decline of these parameters in chest skin. DFMO treatment of transgenic mice from 28 to 32 weeks of age was associated with an absence of ear cancer and a marked regression of dysplastic papillomas. In contrast, the results in chest skin were complex in that the severity of chest precursors diminished, but their incidence was unchanged, and microscopic cancers were still detectable within these lesions. Collectively, this study highlights the utility of multistage epidermal carcinogenesis in K14-HPV16 transgenic mice both for the study of the biology of, and as a screening tool for, novel drugs and chemopreventive regimens.
Compact (Wg/Lg&#x003D;80/85nm) FDSOI 1T-DRAM programmed by Meta Stable Dip (2012)

We demonstrate one of the most compact 1 Transistor DRAM (1T-DRAM) cell on Ultra-Thin-Body and 25nm thin Buried oxide (UTBB) down to a gate width of Wg=80nm and length of L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> =35nm for embedded DRAM applications. We have optimized the programming voltages and studied the influence of the device geometry (Wg, Lg) on the 1T-DRAM performance. The Meta Stable Dip (MSD) method provides high read current margin values, reaching 224μA/μm. This is the first experimental assessment of the MSD approach on such scaled 1T-DRAMs.
Efficacy of an Interdisciplinary Intensive Outpatient Program in Treating Combat-Related Traumatic Brain Injury and Psychological Health Conditions (2021)

<b>Background:</b> Since 2000, over 413,000 US service members (SM) experienced at least one traumatic brain injury (TBI), and 40% of those with in-theater TBIs later screened positive for comorbid psychological health (PH) conditions, including post-traumatic stress disorder (PTSD), depression, and anxiety. Many SMs with these persistent symptoms fail to achieve a recovery that results in a desirable quality of life or return to full duty. Limited information exists though to guide treatment for SMs with a history of mild TBI (mTBI) and comorbid PH conditions. This report presents the methods and outcomes of an interdisciplinary intensive outpatient program (IOP) in the treatment of SMs with combat-related mTBI and PH comorbidities. The IOP combines conventional rehabilitation therapies and integrative medicine techniques with the goal of reducing morbidity in multiple neurological and behavioral health domains and enhancing military readiness. <b>Methods:</b> SMs (<i>n</i> = 1,456) with residual symptoms from mTBI and comorbid PH conditions were treated in a 4-week IOP at the National Intrepid Center of Excellence (NICoE) at Walter Reed National Military Medical Center (WRNMMC). The IOP uses an interdisciplinary, holistic, and patient-centric rehabilitative care model. Interdisciplinary teams provide a diagnostic workup of neurological, psychiatric, and existential injuries, and from these assessments, individualized care plans are developed. Treatment response was assessed using the Neurobehavioral Symptom Inventory (NSI), PTSD Checklist-Military Version (PCL-M), Satisfaction With Life Scale (SWLS), Patient Health Questionnaire-9 (PHQ-9), Generalized Anxiety Disorder-7 (GAD-7), Epworth Sleepiness Scale (ESS), and Headache Impact Test-6 (HIT-6) and administered at admission, discharge, and at 1, 3, and 6 months post-discharge. <b>Findings:</b> Following treatment in the IOP, the symptomatic patients had statistically significant and clinically meaningful improvements across all outcome measures. The largest effect size was seen with GAD-7 (<i>r</i> = 0.59), followed by PHQ-8 (<i>r</i> = 0.56), NSI (<i>r</i> = 0.55), PCL-M (<i>r</i> = 0.52), ESS (<i>r</i> = 0.50), SWLS (<i>r</i> = 0.49), and HIT-6 (<i>r</i> = 0.42). In cross-sectional follow ups, the significant improvements were sustained at 1, 3, and 6 months post-discharge. <b>Interpretation:</b> This report demonstrates that an interdisciplinary IOP achieves significant and sustainable symptom recovery in SMs with combat-related mTBI and comorbid PH conditions and supports the further study of this model of care in complex medical conditions.
Learning to Extract Keyphrases from Text (2002)

Many academic journals ask their authors to provide a list of about five to fifteen key words, to appear on the first page of each article. Since these key words are often phrases of two or more words, we prefer to call them keyphrases. There is a surprisingly wide variety of tasks for which keyphrases are useful, as we discuss in this paper. Recent commercial software, such as Microsoft's Word 97 and Verity's Search 97, includes algorithms that automatically extract keyphrases from documents. In this paper, we approach the problem of automatically extracting keyphrases from text as a supervised learning task. We treat a document as a set of phrases, which the learning algorithm must learn to classify as positive or negative examples of keyphrases. Our first set of experiments applies the C4.5 decision tree induction algorithm to this learning task. The second set of experiments applies the GenEx algorithm to the task. We developed the GenEx algorithm specifically for this task. The third set of experiments examines the performance of GenEx on the task of metadata generation, relative to the performance of Microsoft's Word 97. The fourth and final set of experiments investigates the performance of GenEx on the task of highlighting, relative to Verity's Search 97. The experimental results support the claim that a specialized learning algorithm (GenEx) can generate better keyphrases than a general-purpose learning algorithm (C4.5) and the non-learning algorithms that are used in commercial software (Word 97 and Search 97).
Laser ablation of a platinum target in water. I. Ablation mechanisms (2006)

This is the first in a series of three papers aimed at better understanding the processes that lead to nanomaterial formation during laser ablation of solid targets in liquids. Here we study the variation of the target surface morphology versus laser fluence and wavelength in order to suggest an ablation mechanism. A key finding is that an explosive ablation mechanism is prominent for a wide range of laser fluences for all wavelengths tested. Interestingly, however, ultraviolet (355nm) and infrared (1064nm) wavelengths show characteristically different explosive behaviors. In the infrared case, numerous large craters with diameters around 20μm form at localized points within the laser irradiated area. In contrast, ultraviolet ablation results in a striking transition to nanoscale surface roughness across the entire irradiated area. This texture is attributed to spinodal decomposition at the molten target surface. We propose that the wavelength and fluence dependence of the ablation craters can be explained by the amount of energy absorbed in the target. The consequences of the ablation mechanism for nanomaterial synthesis are discussed.
Cyclosporine in Severe Ulcerative Colitis Refractory to Steroid Therapy (1994)

Intravenous cyclosporine therapy is rapidly effective for patients with severe corticosteroid-resistant ulcerative colitis.
Sialyllactose in Viral Membrane Gangliosides Is a Novel Molecular Recognition Pattern for Mature Dendritic Cell Capture of HIV-1 (2012)

HIV-1 is internalized into mature dendritic cells (mDCs) via an as yet undefined mechanism with subsequent transfer of stored, infectious virus to CD4+ T lymphocytes. Thus, HIV-1 subverts a DC antigen capture mechanism to promote viral spread. Here, we show that gangliosides in the HIV-1 membrane are the key molecules for mDC uptake. HIV-1 virus-like particles and liposomes mimicking the HIV-1 lipid composition were shown to use a common internalization pathway and the same trafficking route within mDCs. Hence, these results demonstrate that gangliosides can act as viral attachment factors, in addition to their well known function as cellular receptors for certain viruses. Furthermore, the sialyllactose molecule present in specific gangliosides was identified as the determinant moiety for mDC HIV-1 uptake. Thus, sialyllactose represents a novel molecular recognition pattern for mDC capture, and may be crucial both for antigen presentation leading to immunity against pathogens and for succumbing to subversion by HIV-1.
A methodology for the ergonomic design of interactive computer graphic systems, and its application to crystallography. (1977)

There are now 15 effective antidepressant medicines marketed in Canada (eight tricyclic antidepressants, three monoamine oxidase inhibitors, and four medicines with novel chemical structures). The tricyclics remain the drug of first choice for major depressions, because of their proven efficacy over three decades, their known side effect profiles, and the cheaper cost of imipramine and amitriptyline compared to other tricyclics and the new antidepressants. The monoamine oxidase inhibitors are an excellent alternative, and are far safer than earlier reports suggested. Maprotiline offers few advantages over the tricyclics and costs significantly more. Trazodone may be a second- or third-line drug with the advantage of minimal anticholinergic properties. Adequate clinical evaluation of nomifensine has not yet occurred. Neuroleptic and cardiotoxic properties of amoxapine suggest other medicines should be tried first.
A method for evaluating incremental utterance understanding in spoken dialogue systems (2002)

In single utterance understanding, which does not include discourse understanding, the concept error rate (CER), or the keyword error rate, has been widely used as an evaluation measure for utterance understanding.However, the CER cannot be used for evaluating systems that understand user utterances based on previous user utterances.In this paper, we propose a method for evaluating incremental utterance understanding, which involves speech recognition, language understanding and discourse processing in spoken dialogue systems, by finding a measure that correlates closely with the system's performance based on dialogue states and their way of update.We defined dialogue performance by task completion time, and performed a multiple linear regression analysis using task completion time as the explained variable and various metrics concerning dialogue states as explaining variables.The obtained multiple regression model fits comparatively well and shows validity as an evaluation measure.
Resin-Bound Dynamic Combinatorial Chemistry (2006)

[reaction: see text] Dynamic combinatorial chemistry (DCC) is a promising technique for receptor-aided selection of high-affinity ligands from equilibrating combinatorial libraries. Identification of the specific ligand(s) selected is often challenging, however, due to difficulties associated with chromatographic separation and/or mass degeneracy within the library. Herein, we describe proof-of-concept experiments demonstrating a new technique termed resin-bound DCC (RB-DCC), which provides a solution to this problem.
Genetic Control of Autoimmune Diabetes in the Nod Mouse (1995)

The nonobese diabetic (NOD) mouse is a model of human autoimmune insulin-dependent diabetes mellitus. The NOD mouse also serves as a model for studying complex polygenic diseases because at least fourteen different loci are linked to disease development. The first Idd locus recognized, Idd1, is linked to the major histocompatibility complex (MHC), and its inheritance and expression are a paradigm for the other non-MHC Idd genes. The NOD allele at Idd1 does not behave as a recessive diabetes susceptibility gene, as it was originally thought to be, but instead it acts as a dominant gene with varying degrees of penetrance for the phenotypes of insulitis, a prediabetic inflammatory lesion, and spontaneous diabetes. MHC congenic strains of mice have shown that the NOD MHC is essential but, by itself, not sufficient for developing diabetes. The contributions of non-MHC Idd loci have also been assessed with NOD congenic strains derived by replacing NOD-specific chromosomal segments with those from diabetes-resistant strains of mice. While only partial protection from disease is provided by resistance alleles at single non-MHC Idd loci, epistatic interaction between two of the loci, Idd3 and Idd10, produced nearly complete protection from diabetes. Identifying Idd genes and defining their biologic functions should further our understanding of autoimmune disease pathogenesis and facilitate development of new treatments for diabetes.
Maximum likelihood successive state splitting (2002)

Modeling contextual variations of phones is widely accepted as an important aspect of a continuous speech recognition system, and much research has been devoted to finding robust models of context for HMM systems. In particular, decision tree clustering has been used to tie output distributions across pre-defined states, and successive state splitting (SSS) has been used to define parsimonious HMM topologies. We describe a new HMM design algorithm, called maximum likelihood successive state splitting (ML-SSS), that combines advantages of both these approaches. Specifically, an HMM topology is designed using a greedy search for the best temporal and contextual splits using a constrained EM algorithm. In Japanese phone recognition experiments, ML-SSS shows recognition performance gains and training cost reduction over SSS under several training conditions.
CAR-T Cells: A Systematic Review and Mixed Methods Analysis of the Clinical Trial Landscape (2017)

CAR-T cells are a promising new therapy that offer significant advantages compared with conventional immunotherapies. This systematic review and clinical trial landscape identifies and critiques published CAR-T cell clinical trials and examines the critical factors required to enable CAR-T cells to become a standard therapy. A review of the literature was conducted to identify suitable studies from the MEDLINE and Ovid bibliographic databases. The literature and database searches identified 20 studies for inclusion. The average number of participants per clinical trial examined was 11 patients. All studies included in this systematic review investigated CAR-T cells and were prospective, uncontrolled clinical studies. Leukemia is the most common cancer subtype and accounts for 57.4% (n = 120) of disease indications. The majority of studies used an autologous cell source (85%, n = 17) rather than an allogeneic cell source. Translational challenges encompass technical considerations relating to CAR-T cell development, manufacturing practicability, clinical trial approaches, CAR-T cell quality and persistence, and patient management.
Towards full automated drive in urban environments: A demonstration in GoMentum Station, California (2017)

Each year, millions of motor vehicle traffic accidents all over the world cause a large number of fatalities, injuries and significant material loss. Automated Driving (AD) has potential to drastically reduce such accidents. In this work, we focus on the technical challenges that arise from AD in urban environments. We present the overall architecture of an AD system and describe in detail the perception and planning modules. The AD system, built on a modified Acura RLX, was demonstrated in a course in GoMentum Station in California. We demonstrated autonomous handling of 4 scenarios: traffic lights, cross-traffic at intersections, construction zones and pedestrians. The AD vehicle displayed safe behavior and performed consistently in repeated demonstrations with slight variations in conditions. Overall, we completed 44 runs, encompassing 110km of automated driving with only 3 cases where the driver intervened the control of the vehicle, mostly due to error in GPS positioning. Our demonstration showed that robust and consistent behavior in urban scenarios is possible, yet more investigation is necessary for full scale rollout on public roads.