Miracle-dz/UniFAR-FTUs huggingface dataset:
Information criterion-based non-hierarchical clustering

In the analysis of actual data, it is important to determine whether there are clusters in the data. This can be done using one of several methods of cluster analysis, which can be roughly divided into hierarchical and nonhierarchical clustering methods. Nonhierarchical clustering can be applied to more types of data than can hierarchical clustering (see e.g., Saito and Yadohisa, 2006), and hence, in this paper, we focus on nonhierarchical clustering. In nonhierarchical clustering, the results heavily depend on the number of clusters, and thus it is very important to select the appropriate number of clusters. Bozdogan (1986) and Manning et al. (2009, Section 16.4.1) used formal information criteria, e.g., Aakaike's information criterion (AIC) and so on, for selecting the number of clusters. In this paper, we verify that such formal information criteria work poorly for selecting the number of clusters by conducting numerical examinations. Hence, we extend a formal AIC by adding a new penalty term, and search for an additional penalty with an acceptable selection-performance through numerical experiments.
Simultaneous determination and anti-inflammatory effects of four phenolic compounds in Dendrobii Herba

Abstract Dendrobii Herba, a traditional Korean medicine, is used for treating atrophic gastritis, diabetes and cardiovascular diseases. Phytochemical studies of Dendrobium species and their compounds have been conducted. However, the pharmaceutical effects of these compounds have not yet been elucidated. We performed quantitative determination of four phenolic compounds, – (1) 4-hydroxybenzoic acid, (2) vanillic acid (3) syringic acid and (4) ferulic acid – in Dendrobii Herba using high-performance liquid chromatography coupled with a photodiode array detector. In addition, we investigated the effects of compounds in LPS-stimulated RAW 264.7 cells by measuring of inflammatory mediators. Among the four compounds, 1–3 had a significant inhibitory effect on TNF-α production. The levels of IL-6 were significantly reduced by treatment with compounds 13 and 4 compared with LPS treated cell. All compounds significantly reduced LPS-stimulated PGE2 production. Thus, these four marker compounds from Dendrobii Herba exhibit anti-inflammatory activity by targeting different inflammation-related cytokines.
VEGF as a potential target in lung cancer

ABSTRACT Introduction The vascular endothelial growth factor A (VEGF) is the main mediator of angiogenesis. In addition, VEGF contributes to cancer growth and metastasis directly targeting tumor cells. VEGF overexpression and/or high VEGF serum levels have been reported in lung cancer. Areas covered We searched Pubmed for relevant preclinical studies with the terms ‘lung cancer’ ‘VEGF’ and ‘in vivo’. We also searched the Clinicaltrials.gov database, the FDA and the EMA websites for the most recent updates on clinical development of anti-VEGF agents. Expert opinion VEGF plays an important role in sustaining the development and progression of lung cancer and it might represent an attractive target for therapeutic strategies. Nevertheless, clinical trials failed to attend the promising expectations deriving from preclinical studies with anti-VEGF agents. To improve the efficacy of anti-VEGF therapies in lung cancer, potential strategies might be the employment of combinatory therapies with immune checkpoint inhibitors or agents that inhibit signaling pathways and proangiogenic factors activated in response to VEGF blockade, and the identification of novel targets in the VEGF cascade. Finally, the identification of predictive markers might help to select patients who are more likely to respond to anti-angiogenic drugs.
Single arm robotic garment folding path generation

Abstract We address the accurate single arm robotic garment folding. The folding capability is influenced mostly by the folding path which is performed by the robotic arm. This paper presents a new method for the folding path generation based on the static equilibrium of forces. The existing approach based on a similar principle confirmed to be accurate for one-dimensional strips only. We generalize the method to two-dimensional shapes by modeling the garment as an elastic shell. The path generated by our method prevents the garment from slipping while folding on a low friction surface. We demonstrate the accuracy of this approach by comparing our paths (a) with the existing method when one-dimensional strips of different materials were modeled, and (b) experimentally with real robotic folding. Graphical Abstract The paper proposes a robotic garment folding path generation procedure. It uses the garment model represented by a thin shell. The path computation seeks states satisfying a static equilibrium condition.
Global spectral clustering in dynamic networks

Significance Statistical theory has mostly focused on static networks observed as a single snapshot in time. In reality, networks are generally dynamic, and it is of substantial interest to discover the clusters within each network to visualize and model their connectivities. We propose the persistent communities by eigenvector smoothing algorithm for detecting time-varying community structure and apply it to a recent dataset in which gene expression is measured during a broad range of developmental periods in rhesus monkey brains. The analysis suggests the existence of change points as well as periods of persistent community structure; these are not well estimated by standard methods due to the small sample size of any one developmental period or region of the brain. Community detection is challenging when the network structure is estimated with uncertainty. Dynamic networks present additional challenges but also add information across time periods. We propose a global community detection method, persistent communities by eigenvector smoothing (PisCES), that combines information across a series of networks, longitudinally, to strengthen the inference for each period. Our method is derived from evolutionary spectral clustering and degree correction methods. Data-driven solutions to the problem of tuning parameter selection are provided. In simulations we find that PisCES performs better than competing methods designed for a low signal-to-noise ratio. Recently obtained gene expression data from rhesus monkey brains provide samples from finely partitioned brain regions over a broad time span including pre- and postnatal periods. Of interest is how gene communities develop over space and time; however, once the data are divided into homogeneous spatial and temporal periods, sample sizes are very small, making inference quite challenging. Applying PisCES to medial prefrontal cortex in monkey rhesus brains from near conception to adulthood reveals dense communities that persist, merge, and diverge over time and others that are loosely organized and short lived, illustrating how dynamic community detection can yield interesting insights into processes such as brain development.
Emerging roles for long noncoding RNAs in skeletal biology and disease

ABSTRACT Normal skeletal development requires tight coordination of transcriptional networks, signaling pathways, and biomechanical cues, and many of these pathways are dysregulated in pathological conditions affecting cartilage and bone. Recently, a significant role has been identified for long noncoding RNAs (lncRNAs) in developing and maintaining cellular phenotypes, and improvements in sequencing technologies have led to the identification of thousands of lncRNAs across diverse cell types, including the cells within cartilage and bone. It is clear that lncRNAs play critical roles in regulating gene expression. For example, they can function as epigenetic regulators in the nucleus via chromatin modulation to control gene transcription, or in the cytoplasm, where they can function as scaffolds for protein-binding partners or modulate the activity of other coding and noncoding RNAs. In this review, we discuss the growing list of lncRNAs involved in normal development and/or homeostasis of the skeletal system, the potential mechanisms by which these lncRNAs might function, and recent improvements in the methodologies available to study lncRNA functions in vitro and in vivo. Finally, we address the likely utility of lncRNAs as biomarkers and therapeutic targets for diseases of the skeletal system, including osteoarthritis, osteoporosis, and in cancers of the skeletal system.
Monograph of Diplachne (Poaceae, Chloridoideae, Cynodonteae)

Abstract Diplachne P. Beauv. comprises two species with C4 (NAD-ME) photosynthesis. Diplachne fusca has a nearly pantropical-pantemperate distribution with four subspecies: D. fusca subsp. fusca is Paleotropical with native distributions in Africa, southern Asia and Australia; the widespread Australian endemic D. f. subsp. muelleri; and D. f. subsp. fascicularis and D. f. subsp. uninervia occurring in the New World. Diplachne gigantea is known from a few widely scattered, older collections in east-central and southern Africa, and although Data Deficient clearly is of conservation concern. A discussion of previous taxonomic treatments is provided, including molecular data supporting Diplachne in its newer, restricted sense. Many populations of Diplachne fusca are highly tolerant of saline substrates and most prefer seasonally moist to saturated soils, often in disturbed areas. Some populations of Diplachne fusca in southern Asia combine nitrogen-fixation, high salinity tolerance and palatibilty to livestock, which should be pursued with further research for purposes of soil reclamation. Diplachne fusca subsp. uninervia is the most invasive of the subspecies and is becoming weedy in some non-native areas, including in the Old World. This monograph provides detailed descriptions of all taxa, a key to the species and subspecies, geographic distributions and information on the anatomy of leaves, stems, lemmatal micromorphology and discussions of the chromosome numbers. Lectotypes are designated for: Atropis carinata Grisb. ; Diplachne acuminata Nash; Diplachne capensis (Nees) Nees var. concinna Nees; Diplachne capensis (Nees) Nees var. obscura Nees, Diplachne capensis (Nees) Nees var. prolifera subvar. minor Nees, Diplachne halei Nash, Diplachne maritima E.P. Bicknel, Diplachne muelleri Benth. , Diplachne reverchonii Vasey, Diplachne tectoneticola Backer, Leptochloa imbricata Thurb. , Leptochloa neuroglossa Peter, Leptochloa uninervia var. typica fo. abbreviata Parodi, Triodia ambigua R. Br. and Triodia parviflora R. Br.
MicroRNA expression and activity in T-cell acute lymphoblastic leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is a lymphoid malignancy caused by the oncogenic transformation of immature T-cell progenitors. Many biologically relevant genetic and epigenetic alterations have been identified as driving factors for this transformation. Recently, microRNAs (miRNAs) have been shown to influence various leukemias, including T-ALL. Aberrant expression of miRNAs can function as either oncogenes or tumor suppressors in T-ALL through the regulation of cell migration, invasion, proliferation, apoptosis, and chemoresistance. This occurs by targeting key signaling pathways or transcriptional factors that play a critical role in T-ALL pathology and progression. Different miRNA expression profiles have been linked to specific genetic subtypes of human T-ALL. Furthermore, miRNAs can also act as independent prognostic factors to predict clinical outcomes for T-ALL patients. In the current review, we will focus on the role of miRNAs in the development and progression of T-ALL.
The Effects of Isopropyl Methylphosphono-Fluoridate (IMPF) Poisoning on Tumor Growth and Angiogenesis in BALB/C Mice

Background Acetylcholinesterase (AChE) and cholinergic receptors have an important role in the immune system and angiogenesis. This work evaluated the effects of isopropyl methylphosphonofluoridate (IMPF), an irreversible inhibitor of AChE, on tumor growth and selected parameters associated with tumor angiogenesis. Material/Methods Experiments were performed on male BALB/c mice exposed to IMPF (study group) or saline buffer (control group) and inoculated with L-1 sarcoma; the number of new blood vessels (TIA test) and the level of αvβ3 integrin (131I-MAb-antiβ3 assay) were analyzed at seven, 14, or 21 days after implantation of the tumor cells. Results The IMPF poisoning affected tumor angiogenesis (TIA test). There was a statistically significant increase in the number of newly forming blood vessels in the group subjected to IMPF and inoculated with tumor cells. Conclusions This study showed that IMPF had a significant effect on the regulation of lymphocyte-induced angiogenesis and the modulation of angiogenic and pro-inflammatory cytokines secretion. The observed effects suggest involvement of neuronal and/or non-neuronal cholinergic signaling pathway.
Modeling Patterns for Performance Analysis of Production and Safety Systems in Process Industry. (Modélisation des patterns d'analyse des performances des systèmes de production et de sûreté de fonctionnement dans l'industrie des procédés)

Les systemes de production et de surete de fonctionnement sont d'une importance majeure dans l'industrie des procedes. Leurs performances impactent directement les interets de l'industrie. Ces systemes ont des comportements similaires. Ces comportements peuvent etre conceptualises dans des modeles via des patterns de modelisation. La reutilisation de ces patterns permet de rendre le processus de modelisation a la fois simplifiee et plus efficace.Dans cette these, nous proposons un ensemble varie de patterns de modelisation. Ils sont classes en fonction de leur usage, ce qui reflete le fonctionnement d'un pattern de modelisation. Les patterns sont presentes sous forme d’un catalogue. Sur la base de l'etude de nombreux systemes de production et de securite, vingt-quatre (24) patterns de modelisation sont introduits. Chaque pattern est represente par un ensemble d'elements structures. Nous proposons une methodologie basee sur les patterns pour l'analyse des performances des systemes de production et de surete de fonctionnement.Pour tester la pertinence des patterns de modelisation suggeres, nous avons mene des etudes experimentales sur un ensemble de systemes de production et de surete. Tous les systemes de validation sont extraits de la litterature. Ces systemes traitent la majorite des difficultes de modelisation detectees auparavant. Une comparaison est effectuee entre les resultats obtenus en utilisant la modelisation basee sur les patterns et ceux rapportes dans la litterature.
New Insights in Purinergic Therapy: Novel Antagonists for UTP-Activated P2Y Receptors from Natural Products

P2Y2 and P2Y4 receptors are physiologically activated by UTP and are widely expressed in many cell types in humans. They promote an increase in intracellular calcium via PLCβ/ IP3 and act on ion flux and water secretion. P2Y2 plays an important role in inflammation and proliferation of tumor cells, which could be attenuated with the use of antagonists. However, little is known about the physiological functions related to P2Y4 due to the lack of selective ligands for these receptors, which can be solved through the search of novel compounds with antagonistic activity. In the present study, we have applied a methodology of calcium measurement to identify new antagonist candidates for these receptors. Firstly, we established optimal conditions for calcium assay using J774.G8, a murine macrophage cell line, which expresses functional P2Y2 and P2Y4 receptors. J774.G8 cells were loaded with 2 μM of Fluo-4 to test its sensitivity in responding calcium stimuli. ATP and ionomycin, known as inductors of intracellular calcium rise, were used to stimulate cells. The EC50 obtained were 11 μM and 103 nM, respectively. Subsequently, investigation of P2Y2 and P2Y4 expression was performed. These cells responded with EC50 of 1.021 μM to the UTP stimulation. Screening assays were performed and a total of 100 extracts from Brazilian natural products were tested. JA2, RA3, and RB3 extracts stood out for their ability to inhibit UTP-induced responses without causing cytotoxicity and presented IC50 of 32.32 μg/mL, 14.99 μg/mL, and 12.98 μg/mL, respectively. Collectively, our results point to the discovery of potential antagonists candidates from natural products for UTPactivated receptors.
Folate deficiency induces mitotic aberrations and chromosomal instability by compromising the spindle assembly checkpoint in cultured human colon cells

Folates comprise the essential B9 vitamin that act as cofactors and cosubstrates in one-carbon metabolism for both biosynthesis and methylation of DNA and RNA. Folate deficiency (FD) has been shown to induce chromosomal instability (CIN), yet the underlying mechanisms are poorly understood. Here, we used human NCM460 colon mucosal cells as a model to investigate the effect of FD on spindle assembly checkpoint (SAC), a cell-cycle regulatory pathway preventing CIN during mitosis. Cells were maintained in medium containing 1.36 (FD) and 2260 nM (control, FC) folate for 21 days. CIN was measured by cytokinesis-block micronucleus assay; mitotic infidelity was determined by aberrant mitosis analysis; SAC activity was assessed by nocodazole-challenge assay, and the expression of core SAC genes was examined by real-time quantitative PCR (RT-qPCR). We found that, relative to FC, FD significantly induced CIN in a time-dependent way (P < 0.01). Mitotic cells cultured in FD medium had significant higher frequencies of misalignment, misegregation and spindle multipolarity than those cultured in FC medium (P < 0.01). FD-induced SAC impairment and overriding, resulting premature mitotic exit and cell multinucleation (P < 0.05). Moreover, FD deregulated the expression of several key SAC genes (P < 0.01). Overall, these data are the first to demonstrate that FD substantially compromises SAC network which predisposes cells to mitotic aberrations and CIN. These results establish a new link between folate metabolism and SAC signalling, two pathways that are highly relevant for tumorigenesis.
First-Line Vinorelbine-Mitoxantrone Combination in Metastatic Breast Cancer Patients Relapsing after an Adjuvant Anthracycline Regimen: Results of a Phase II Study

Purpose: Previous studies demonstrated that doxorubicin and vinorelbine combinations in first-line chemotherapy are highly active in metastatic breast cancer. Mitoxantrone is an anthracenedione with low cardiotoxicity, and seems to be effective when combined with vinorelbine after prior exposure to anthracyclines. Patients and Methods: Seventy-two patients with metastatic breast cancer were included in a phase II study. All patients had previously received one anthracycline-containing regimen (doxorubicin or epirubicin) in an adjuvant setting. Vinorelbine was administered at 25 mg/m2 in a 20-min intravenous (i.v.) infusion, days 1 and 8. Mitoxantrone was given at 10 mg/m2 (66 patients) or 12 mg/m2 (6 patients) in a slow i.v. infusion on day 1. Courses were repeated every 3 weeks. Results: Sixty-five patients were evaluable for response; the objective response rate was 49% (95% CI: 37–63%), including four complete and 28 partial responses, with a median duration of response of 7 months (range 2.3–27). Median overall survival was 19 months (range 2–48). Grade 3–4 granulocytopenia was observed in 46% of patients. There were 12 admissions (3% of cycles), involving 17% of patients for febrile neutropenia. Seven patients (10%) experienced grade 3 or 4 cardiotoxicity, and 1 patient died of cardiac heart failure. Other side effects were rare and mild. Conclusions: The vinorelbine and mitoxantrone combination is an active regimen with low toxic complications when cumulative doses of mitoxantrone are limited to 70 mg/m2. The results in this phase II study make it worthwhile including this regimen in a phase III study for patients who have previously received an anthracycline-containing regimen.
Maintenance of Distal Intestinal Structure in the Face of Prolonged Fasting: A Comparative Examination of Species From Five Vertebrate Classes

It was recently shown that fasting alters the composition of microbial communities residing in the distal intestinal tract of animals representing five classes of vertebrates [i.e., fishes (tilapia), amphibians (toads), reptiles (leopard geckos), birds (quail), and mammals (mice)]. In this study, we tested the hypothesis that the extent of tissue reorganization in the fasted distal intestine was correlated with the observed changes in enteric microbial diversity. Segments of intestine adjacent to those used for the microbiota study were examined histologically to quantify cross‐sectional and mucosal surface areas and thicknesses of mucosa, submucosa, and tunica muscularis. We found no fasting‐induced differences in the morphology of distal intestines of the mice (3 days), quail (7 days), or geckos (28 days). The toads, which exhibited a general increase in phylogenetic diversity of their enteric microbiota with fasting, also exhibited reduced mucosal circumference at 14 and 21 days of fasting. Tilapia showed increased phylogenetic diversity of their enteric microbiota, and showed a thickened tunica muscularis at 21 days of fasting; but this morphological change was not related to microbial diversity or absorptive surface area, and thus, is unlikely to functionally match the changes in their microbiome. Given that fasting caused significant increases and reductions in the enteric microbial diversity of mice and quail, respectively, but no detectable changes in distal intestine morphology, we conclude that reorganization is not the primary factor shaping changes in microbial diversity within the fasted colon, and the observed modest structural changes are more related to the fasted state. Anat Rec, 300:2208–2219, 2017. © 2017 Wiley Periodicals, Inc.
Preliminary evidence of attenuated blood pressure reactivity to acute stress in adults following a recent marital separation

Objective: This study explores cardiovascular reactivity during an acute-stress task in a sample of recently separated adults. Design: In a cross-sectional design, we examined the association between adults’ subjective separation-related distress and changes in heart rate and blood pressure across the acute-stress laboratory paradigm in a sample of 133 (n = 49 men) recently separated adults. Main outcome measures: Heart rate (HR) and Blood pressure (BP) were recorded across a resting baseline period, a math stressor task, and a recovery period. Results: Multilevel analyses revealed that adults who reported greater separation-related distress exhibited higher initial BP and a slower linear increase in BP across the study period. In addition, adults reporting greater separation-related distress evidenced significantly slower declines in diastolic blood pressure (DBP) following the acute-stress task. HR reactivity was not moderated by separation-related distress. Conclusions: In recently separated adults, preliminary evidence suggests that the context of the stressors may reveal differential patterns of problematic reactivity (exaggerated or blunted responding). Greater emotional intrusion and hyperactivity symptoms may index increased risk for blunted cardiovascular reactivity to general stressors. This pattern of reactivity is consistent with models of allostatic load that emphasise the deleterious effect of hyporesponsivity to environmental demands.