Miracle-dz/UniFAR-FTUs huggingface dataset:
High Macrophage Infiltration along the Tumor Front Correlates with Improved Survival in Colon Cancer

Purpose: The role of macrophages in tumorigenesis is complex because they can both prevent and promote tumor development. Experimental Design: Four hundred forty-six colorectal cancer specimens were stained with the pan-monocyte/macrophage marker CD68, and average infiltration along the tumor front was semiquantitatively evaluated using a four-grade scale. Each section was similarly scored for the presence of CD68 hotspots. Some aspects of macrophage-tumor cell interactions were also studied using in vitro coculture systems. Results: Including all patients, regardless of surgical outcome and localization, survival increased incrementally with CD68TFMean infiltration grade (P = 0.0001) but not in curatively resected colon cancers (P = 0.28). CD68 hotspot score (CD68TFHotspot) was divided into high and low. A high hotspot score conferred a highly significant survival advantage also in curatively resected colon cancer cases (n = 199, P = 0.0002) but not in rectal cancers. CD68TFHotspot high turned out as an independent prognostic marker for colon cancer in multivariate analyses including gender, age, localization, grade, stage, tumor type, and lymphocytes at the tumor front, conferring a relative risk of 0.49 (P = 0.007). In vitro coculture experiments, using phorbol 12-myristate 13-acetate–activated U937 cells as macrophage model, revealed that a high ratio of macrophages to colon cancer cells inhibited cancer cell growth. This was partially dependent on cell-to-cell contact, whereas Boyden chamber cocultivation without cell-to-cell contact promoted cancer cell spread. Conclusions: In conclusion, our data indicate that a dense macrophage infiltration at the tumor front positively influences prognosis in colon cancer and that the degree of cell-to-cell contact may influence the balance between protumorigenic and antitumorigenic properties of macrophages.
Updates on the Clinical Evidenced Herb-Warfarin Interactions

Increasing and inadvertent use of herbs makes herb-drug interactions a focus of research. Concomitant use of warfarin, a highly efficacious oral anticoagulant, and herbs causes major safety concerns due to the narrow therapeutic window of warfarin. This paper presents an update overview of clinical findings regarding herb-warfarin interaction, highlighting clinical outcomes, severity of documented interactions, and quality of clinical evidence. Among thirty-eight herbs, Cannabis, Chamomile, Cranberry, Garlic, Ginkgo, Grapefruit, Lycium, Red clover, and St. John's wort were evaluated to have major severity interaction with warfarin. Herbs were also classified on account of the likelihood of their supporting evidences for interaction. Four herbs were considered as highly probable to interact with warfarin (level I), three were estimated as probable (level II), and ten and twenty-one were possible (level III) and doubtful (level IV), respectively. The general mechanism of herb-warfarin interaction almost remains unknown, yet several pharmacokinetic and pharmacodynamic factors were estimated to influence the effectiveness of warfarin. Based on limited literature and information reported, we identified corresponding mechanisms of interactions for a small amount of “interacting herbs. ” In summary, herb-warfarin interaction, especially the clinical effects of herbs on warfarin therapy should be further investigated through multicenter studies with larger sample sizes.
Brain DA D2 receptors predict reinforcing effects of stimulants in humans: Replication study

We had shown that striatal DA D2 receptors levels predicted the reinforcing responses to the psychostimulant drug methylphenidate in nondrug‐abusing subjects. Here, we assessed the replicability of this finding. We measured D2 receptors with PET and [11C]raclopride (twice to determine stability) in seven nondrug‐abusing subjects to assess if they predicted the self‐reports of “drug‐liking” to intravenous methylphenidate (0.5 mg/kg). DA D2 measures were significantly correlated with “drug‐liking” in both evaluations (r = 0.82 and r = 0.78); subjects with the lowest levels reported the higher ratings of “drug‐liking” and vice versa. These results replicate our previous findings and provide further evidence that striatal DA D2 receptors modulate reinforcing responses to stimulants in humans and may underlie predisposition for drug self‐administration. Synapse 46:79–82, 2002. © 2002 Wiley‐Liss, Inc.
Monitoring for Cardiovascular Disease in Survivors of Childhood Cancer: Report From the Cardiovascular Disease Task Force of the Children's Oncology Group

Curative therapy for childhood cancer has improved significantly in the last 2 decades such that, at present, ∼80% of all children with cancer are likely to survive ≥5 years after diagnosis. Prevention, early diagnosis, and treatment of long-term sequelae of therapy have become increasingly more significant as survival rates continue to improve. Cardiovascular disease is a well-recognized cause of increased late morbidity and mortality among survivors of childhood cancer. The Children's Oncology Group Late Effects Committee and Nursing Discipline and Patient Advocacy Committee have recently developed guidelines for follow-up of long-term survivors of pediatric cancer. A multidisciplinary task force critically reviewed the existing literature to evaluate the evidence for the cardiovascular screening recommended by the Children's Oncology Group guidelines. In this review we outline the clinical manifestations of late cardiovascular toxicities, suggest modalities and frequency of monitoring, and address some of the controversial and unresolved issues regarding cardiovascular disease in childhood cancer survivors.
4E-Binding Protein 1, A Cell Signaling Hallmark in Breast Cancer that Correlates with Pathologic Grade and Prognosis

Purpose: Cell signaling pathways include a complex myriad of interconnected factors from the membrane to the nucleus, such as erbB family receptors and the phosphoinositide-3-kinase/Akt/mTOR and Ras-Raf-ERK cascades, which drive proliferative signals, promote survival, and regulate protein synthesis. Experimental Design: To find pivotal factors in these pathways, which provide prognostic information in malignancies, we studied 103 human breast tumors with an immunohistochemical profile, including total and phosphorylated (p) proteins: human epidermal growth factor receptor 2 (HER2), epidermal growth factor receptor, extracellular signal-regulated kinase 1/2, Akt, 4E-binding protein 1 (4EBP1), eukaryotic initiation factor 4E, phosphorylated ribosomal protein S6 kinase 1, phosphorylated ribosomal protein S6, and Ki67. Western blot and reverse lysate protein arrays were also done in a subset of tumors. Results: Significantly, activation of the phosphoinositide-3-kinase/Akt/mTOR cascade was detected in a high proportion of tumors (41.9%). Tumors with HER2 overexpression showed higher p-Akt as compared with negative tumors (P < 0.001). Levels of p-Akt correlated with the downstream molecules, p-4EBP1 (P = 0.001) and p-p70S6K (P = 0.05). Although 81.5% of tumors expressed p-4EBP1, in 16.3% of these tumors, concomitant activation of the upstream factors was not detected. Interestingly, p-4EBP1 was mainly expressed in poorly differentiated tumors (P < 0.001) and correlated with tumor size (P < 0.001), presence of lymph node metastasis (P = 0.002), and locoregional recurrences (P = 0.002). Coexpression of p-4EBP1 and p-eIF4G correlated with a high tumor proliferation rate (P = 0.012). Conclusion: In this study, p-4EBP1 was the main factor in signaling pathways that associate with prognosis and grade of malignancy in breast tumors. Moreover, p-4EBP1 was detected in both HER2-positive and HER2-negative tumors. This factor seems to be a channeling point at which different upstream oncogenic alterations converge and transmit their proliferative signal, modulating protein translation.
Spatially varying relationships between surface urban heat islands and driving factors across cities in China

Global regression models, such as Ordinary Least Squares, are generally used to explore driving factors of surface urban heat island (SUHI) effects across large cities on a national level, but issues of spatial non-stationarity or local variations have rarely been taken into account. Our study quantifies SUHI effects for 274 cities in China with MODIS LST products and explores spatially varying relationships between SUHI intensity (SUHII) and their driving factors using geographically weighted regression (GWR). The results show that GWR models have stronger explanatory power and lower spatial autocorrelations of residuals compared with ordinary least square models; the application of GWR models finds that the relationships between SUHII and the driving factors vary across China. Spatially varying coefficients from GWR models could contribute to the development of local-specific urban planning or policies in different regions. The findings from our investigation suggest that GWR has the potential to serve as a useful tool for environmental investigations on a national scale.
Chemical Pesticides and Human Health: The Urgent Need for a New Concept in Agriculture

The industrialization of the agricultural sector has increased the chemical burden on natural ecosystems. Pesticides are agrochemicals used in agricultural lands, public health programs, and urban green areas in order to protect plants and humans from various diseases. However, due to their known ability to cause a large number of negative health and environmental effects, their side effects can be an important environmental health risk factor. The urgent need for a more sustainable and ecological approach has produced many innovative ideas, among them agriculture reforms and food production implementing sustainable practice evolving to food sovereignty. It is more obvious than ever that the society needs the implementation of a new agricultural concept regarding food production, which is safer for man and the environment, and to this end, steps such as the declaration of Nyéléni have been taken.
Altered Auditory BOLD Response to Conspecific Birdsong in Zebra Finches with Stuttered Syllables

How well a songbird learns a song appears to depend on the formation of a robust auditory template of its tutor's song. Using functional magnetic resonance neuroimaging we examine auditory responses in two groups of zebra finches that differ in the type of song they sing after being tutored by birds producing stuttering-like syllable repetitions in their songs. We find that birds that learn to produce the stuttered syntax show attenuated blood oxygenation level-dependent (BOLD) responses to tutor's song, and more pronounced responses to conspecific song primarily in the auditory area field L of the avian forebrain, when compared to birds that produce normal song. These findings are consistent with the presence of a sensory song template critical for song learning in auditory areas of the zebra finch forebrain. In addition, they suggest a relationship between an altered response related to familiarity and/or saliency of song stimuli and the production of variant songs with stuttered syllables.
Ecoregional and Archetypical Considerations for National Responses to Food Security under Climate Change

Yu-Pin Lin 1,* ID , Josef Settele 2 and Joy R. Petway 1 1 Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan; d05622007@ntu.edu. tw 2 Department of Community Ecology, Helmholtz-Centre for Environmental Research—UFZ Theodor-Lieser-Str. 4, 06120 Halle, Germany; josef.settele@ufz.de * Correspondence: yplin@ntu.edu. tw; Tel. : +886-2-33663467
Gait and Quiet-Stance Performance Among Adolescents After Concussion-Symptom Resolution.

CONTEXT Concussions affect a large number of US athletes each year. Returning an athlete to activity once self-reported symptoms have resolved can be problematic if unrecognized neurocognitive and balance deficits persist. Pairing cognitive and motor tasks or cognitive and quiet-stance tasks may allow clinicians to detect and monitor these changes postconcussion. OBJECTIVE To prospectively examine adolescent athletes' gait and quiet-stance performance while concurrently completing a cognitive task acutely after concussion and after symptom resolution. DESIGN Case-control study. SETTING Sport concussion clinic. PATIENTS OR OTHER PARTICIPANTS Thirty-seven athletes (age = 16.2 ± 3.1 years; 54% female) were diagnosed with a concussion, and their performance was compared with that of a group of 44 uninjured control participants (age = 15.0 ± 2.0 years; 57% female). INTERVENTION Participants diagnosed with a concussion completed a symptom inventory and single- and dual-task gait and quiet-stance evaluations within 21 days of injury and then again after symptom resolution. Gait and postural-control measurements were quantified using an inertial sensor system and analyzed using multivariate analyses of covariance. MAIN OUTCOME MEASURE(S) Post-Concussion Symptom Scale, single-task and dual-task gait measures, quiet-stance measures, and cognitive task performance. RESULTS At the initial postinjury examination, single-task gait stride length (1.16 ± 0.14 versus 1.25 ± 0.13 m, P = .003) and dual-task gait stride length (1.02 ± 0.13 m versus 1.10 ± 0.13 m, P = .011) for the concussion group compared with the control group, respectively, were shorter. After symptom resolution, no single-task gait differences were found, but the concussion group demonstrated slower gait velocity (0.78 ± 0.15 m/s versus 0.92 ± 0.14 m/s, P = .005), lower cadence (92.5 ± 12.2 steps/min versus 99.3 ± 7.8 steps/min, P < .001), and a shorter stride length (0.99 ± 0.15 m versus 1.10 ± 0.13 m, P = .003) during dual-task gait than the control group. No between-groups differences were detected during quiet stance at either time point. CONCLUSIONS Acutely after concussion, single-task and dual-task stride-length alterations were present among youth athletes compared with a control group. Although single-task gait alterations were not detected after symptom resolution, dual-task gait differences persisted, suggesting that dual-task gait alterations may persist longer after concussion than single-task gait or objective quiet-stance alterations. Dual-task gait assessments may, therefore, be a useful component in monitoring concussion recovery after symptom resolution.
Towards Evaluation of Security Assurance during the Software Development Lifecycle

It is difficult to state whether a certain software productis developed securely enough. An evaluation methodology that takes the security assurance methods used during the software development lifecycle into account is one step closer to a solution to this problem. In this paper we discuss our first heuristics for security assurance evaluation that would give guidelines on the trustworthiness of the software development lifecycle. The input for evaluations include the context, expert opinions, outcome of the methods and reputation. Our evaluation heuristics are a step towards being able to deduce about the level of assurance for a software process, compared to a certain context-specific baseline.
Large Deformation Diffeomorphic Metric Mapping Registration of Reconstructed 3D Histological Section Images and in vivo MR Images

Our current understanding of neuroanatomical abnormalities in neuropsychiatric diseases is based largely on magnetic resonance imaging (MRI) and post mortem histological analyses of the brain. Further advances in elucidating altered brain structure in these human conditions might emerge from combining MRI and histological methods. We propose a multistage method for registering 3D volumes reconstructed from histological sections to corresponding in vivo MRI volumes from the same subjects: (1) manual segmentation of white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF) compartments in histological sections, (2) alignment of consecutive histological sections using 2D rigid transformation to construct a 3D histological image volume from the aligned sections, (3) registration of reconstructed 3D histological volumes to the corresponding 3D MRI volumes using 3D affine transformation, (4) intensity normalization of images via histogram matching, and (5) registration of the volumes via intensity based large deformation diffeomorphic metric (LDDMM) image matching algorithm. Here we demonstrate the utility of our method in the transfer of cytoarchitectonic information from histological sections to identify regions of interest in MRI scans of nine adult macaque brains for morphometric analyses. LDDMM improved the accuracy of the registration via decreased distances between GM/CSF surfaces after LDDMM (0.39 ± 0.13 mm) compared to distances after affine registration (0.76 ± 0.41 mm). Similarly, WM/GM distances decreased to 0.28 ± 0.16 mm after LDDMM compared to 0.54 ± 0.39 mm after affine registration. The multistage registration method may find broad application for mapping histologically based information, for example, receptor distributions, gene expression, onto MRI volumes.
Hope and Related Variables in Italian Cancer Patients

Hope, long considered an essential element for life, has been shown to be important among cancer patients in coping, perceived control over the illness, and psychologic adjustment to the illness. The purpose of this study was (a) to describe the level of hope in Italian cancer patients; (b) to compare the levels of hope during and after hospitalization; (c) to determine whether hope was correlated with quality of life and several symptoms; and (d) to determine whether the variables from the international literature also pertain to Italian cancer patients. A descriptive correlational design using repeated measures was chosen to study 80 Italian cancer patients during hospitalization and then at home. The following instruments were used: a Sociodemographic Questionnaire, the Hope Related Variable Questionnaire, the Nowotny Hope Scale, the Rotterdam Symptom Checklist, and the Hospital Anxiety and Depression Scale. Overall, patients were moderately hopeful and the level of hopefulness was similar in the hospital and at home. Hope was positively correlated with quality of life, self-esteem, coping, adjustment to the illness, well-being, comfort in the hospital, satisfaction with information received, relationship with, and support from family, healthcare professional, and friends. Hope was negatively correlated with anxiety, depression, and boredom during hospitalization. Time since diagnosis, illness stage, and knowing or not knowing the diagnosis and treatment were not correlated with hope. Similarities and differences with the international literature are discussed, and implications for caring for Italian cancer patients are drawn.
Machine reading of camera-held low quality text images: An ICA-based image enhancement approach for improving OCR accuracy

An Independent Component Analysis (ICA)-based image enhancement technique is presented to improve the accuracy for machine reading of camera-based images. Images of inscriptions that are normally engraved on stones or other durable materials and found at the sites of historical monuments are taken as a reference for conducting the present experiments. Significant improvement in recognition rate of a commercial OCR system shows the potential of the proposed ICA-based method. It improves word and character recognition accuracies of the OCR system by 68.6% (from 11.2% to 79.8%) and 57.3% (from 34.8% to 92.1%), respectively.
A HIGH ACCURACY LERAY-DECONVOLUTION MODEL OF TURBULENCE AND ITS LIMITING BEHAVIOR

In 1934, J. Leray proposed a regularization of the Navier–Stokes equations whose limits were weak solutions of the Navier–Stokes equations. Recently, a modification of the Leray model, called the Leray-alpha model, has attracted interest for turbulent flow simulations. One common drawback of the Leray type regularizations is their low accuracy. Increasing the accuracy of a simulation based on a Leray regularization requires cutting the averaging radius, i.e. remeshing and resolving on finer meshes. This article analyzes on a family of Leray type models of arbitrarily high orders of accuracy for a fixed averaging radius. We establish the basic theory of the entire family including limiting behavior as the averaging radius decreases to zero (a simple extension of results known for the Leray model). We also give a more technically interesting result on the limit as the order of the models increases with a fixed averaging radius. Because of this property, increasing the accuracy of the model is potentially cheaper than decreasing the averaging radius (or meshwidth) and high order models are doubly interesting.
Engineering Motif Search for Large Graphs

In the graph motif problem, we are given as input a vertex-colored graph H (the host graph) and a multiset of colors M (the motif). Our task is to decide whether H has a connected set of vertices whose multiset of colors agrees with M. The graph motif problem is NP-complete but known to admit parameterized algorithms that run in linear time in the size of H. We demonstrate that algorithms based on constrained multilinear sieving are viable in practice, scaling to graphs with hundreds of millions of edges as long as M remains small. Furthermore, our implementation is topology-invariant relative to the host graph H, meaning only the most crude graph parameters (number of edges and number of vertices) suffce in practice to determine the algorithm performance.
Assessing the impact of reactive workloads on the performance of Web applications

Designing systems with better performance and scalability is a real need to fulfill the user demands and generate profitable Web services. Being able to mimic user behavior and the workload they generate on the servers is fundamental to evaluate the performance of systems and their improvements. One aspect that is usually neglected by workload generators is the user reactivity, that is, how the users react to variable server response time. Further, it is not clear how the reactivity-related changes in the user generated workload affect the server and how these dependences converge. This paper addresses this problem by proposing, implementing, and validating a workload generator that accounts for reactivity while interacting with servers. Our workload generator is used, for instance, to generate workloads based on a TPC-W benchmark. These workloads are used to assess the impacts of reactivity on the performance of a Web application. The results show significant changes in terms of throughput and response time for the experiments, raising the possibility of improving the performance of Web systems considering user reactivity.
An Efficient Implementation of the BSP Programming Library for VIA

Virtual Interface Architecture(VIA) is a light-weight protocol for protected user-level zero-copy communication. In spite of the promised high performance of VIA, previous MPI implementations for GigaNet's cLAN revealed low communication performance. Two main sources of such low performance are the discrepancy in the communication model between MPI and VIA and the multi-threading overhead. In this paper, we propose a new implementation of the Bulk Synchronous Parallel(BSP) programming library for VIA called xBSP to overcome such problems. To the best of our knowledge, xBSP is the first implementation of the BSP library for VIA. xBSP demonstrates that the selection of a proper library is important to exploit the features of light-weight protocols. Intensive use of Remote Direct Memory Access(RDMA) operations leads to high performance close to the native VIA performance with respect to round trip delay and bandwidth. Considering the effects of multi-threading, memory registration, and completion policy on performance, we could obtain an efficient BSP implementation for cLAN, which was confirmed by experimental results.