Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping and Attributing Normalized Difference Vegetation Index Trends for Nepal

Global change affects vegetation cover and processes through multiple pathways. Long time series of surface land surface properties derived from satellite remote sensing give unique abilities to observe these changes, particularly in areas with complex topography and limited research infrastructure. Here, we focus on Nepal, a biodiversity hotspot where vegetation productivity is limited by moisture availability (dominated by a summer monsoon) at lower elevations and by temperature at high elevations. We analyze the normalized difference vegetation index (NDVI) from 1981 to 2015 semimonthly, at an 8 km spatial resolution. We use a random forest (RF) of regression trees to generate a statistical model of the NDVI as a function of elevation, land use, CO 2 level, temperature, and precipitation. We find that the NDVI increased over the studied period, particularly at low and middle elevations and during the fall (post-monsoon). We infer from the fitted RF model that the NDVI linear trend is primarily due to CO 2 level (or another environmental parameter that is changing quasi-linearly), and not primarily due to temperature or precipitation trends. On the other hand, interannual fluctuation in the NDVI is more correlated with temperature and precipitation. The RF accurately fits the available data and shows promise for estimating trends and testing hypotheses about their causes.
Chromosome positioning from activity-based segregation

Chromosomes within eukaryotic cell nuclei at interphase are not positioned at random, since gene-rich chromosomes are predominantly found towards the interior of the cell nucleus across a number of cell types. The physical mechanisms that could drive and maintain the spatial segregation of chromosomes based on gene density are unknown. Here, we identify a mechanism for such segregation, showing that the territorial organization of chromosomes, another central feature of nuclear organization, emerges naturally from our model. Our computer simulations indicate that gene density-dependent radial segregation of chromosomes arises as a robust consequence of differences in non-equilibrium activity across chromosomes. Arguing that such differences originate in the inhomogeneous distribution of ATP-dependent chromatin remodeling and transcription machinery on each chromosome, we show that a variety of non-random positional distributions emerge through the interplay of such activity, nuclear shape and specific interactions of chromosomes with the nuclear envelope. Results from our model are in reasonable agreement with experimental data and we make a number of predictions that can be tested in experiments.
The K-Means Algorithm Evolution

Clustering is one of the main methods for getting insight on the underlying nature and structure of data. The purpose of clustering is organizing a set of data into clusters, such that the elements in each cluster are similar and different from those in other clusters. One of the most used clustering algorithms presently is K -means, because of its easiness for interpreting its results and implementation. The solution to the K -means clustering problem is NP-hard, which justifies the use of heuristic methods for its solution. To date, a large number of improvements to the algorithm have been proposed, of which the most relevant were selected using systematic review methodology. As a result, 1125 documents on improvements were retrieved, and 79 were left after applying inclusion and exclusion criteria. The improvements selected were classified and summarized according to the algorithm steps: initialization, classification, centroid calculation, and convergence. It is remarkable that some of the most successful algorithm variants were found. Some articles on trends in recent years were included, concerning K -means improvements and its use in other areas. Finally, it is considered that the main improvements may inspire the development of new heuristics for K -means or other clustering algorithms.
Changing T-cell enigma: Cancer killing or cancer control?

Data from different laboratories and theoretical considerations challenge our current view on anticancer immunity. Immune cells are capable of destroying cancer cells under in vitro and in vivo conditions. Therefore, cellular immunity is considered to control cancers through mechanisms that kill cancers. Yet, therapeutic anticancer immune responses rarely delete cancers. If efficient, they rather establish a life with stable disease. This raises the question of whether killing is the sole mechanism by which immune therapy attacks cancers. Here, we show that, besides cancer eradication by cytotoxic lymphocytes, other modes of action are operative and strictly required for cancer control. We show that T helper-1 cells arrest cancer growth by driving cancers into a state of stable or permanent growth arrest, called senescence. Such immune cells establish cytokine-producing walls around developing cancers. When producing interferon-γ and tumor necrosis factor, this cytokine-induced tumor immune-surveillance keeps the cancer cells in a permanently non-proliferating state. Simultaneously, antiangiogenic chemokines cut their connections to the surrounding tissues. This strategy significantly reduces tumor burden and prolongs life of cancer-bearing animals. As human cancers also undergo senescence, the current data suggest tumor-immune surveillance through cytokine-induced senescence, instead of tumor eradication, as the more realistic and primary goal of cancer control.
Human neuroblastoma cell lines as models for the in vitro study of neoplastic and neuronal cell differentiation.

Neuroblastoma is a childhood solid tumor composed of primitive cells derived from precursors of the autonomic nervous system. This neoplasm has the highest rate of spontaneous regression of all cancer types and has been noted to undergo spontaneous and chemically induced differentiation into elements resembling mature nervous tissue. As such, neuroblastoma has been a prime model system for the study of neuronal differentiation and the process of cancer cell maturation. In this paper we review those agents that have been described to induce the differentiation of neuroblastoma, with an emphasis on the effects and possible mechanisms of action of a group of related compounds, the retinoids. With this model system and the availability of subclones that are both responsive and resistant to chemically induced differentiation, fundamental questions regarding the mechanisms and processes underlying cell maturation have become more amenable to in vitro study. ImagesFIGURE 1. AFIGURE 1. BFIGURE 1. CFIGURE 2. AFIGURE 2. B
Palmitoylation of tetraspanin proteins: modulation of CD151 lateral interactions, subcellular distribution, and integrin-dependent cell morphology.

Here we demonstrate that multiple tetraspanin (transmembrane 4 superfamily) proteins are palmitoylated, in either the Golgi or a post-Golgi compartment. Using CD151 as a model tetraspanin, we identified and mutated intracellular N-terminal and C-terminal cysteine palmitoylation sites. Simultaneous mutations of C11, C15, C242, and C243 (each to serine) eliminated >90% of CD151 palmitoylation. Notably, palmitoylation had minimal influence on the density of tetraspanin protein complexes, did not promote tetraspanin localization into detergent-resistant microdomains, and was not required for CD151-alpha 3 beta 1 integrin association. However, the CD151 tetra mutant showed markedly diminished associations with other cell surface proteins, including other transmembrane 4 superfamily proteins (CD9, CD63). Thus, palmitoylation may be critical for assembly of the large network of cell surface tetraspanin-protein interactions, sometimes called the "tetraspanin web. " Also, compared with wild-type CD151, the tetra mutant was much more diffusely distributed and showed markedly diminished stability during biosynthesis. Finally, expression of the tetra-CD151 mutant profoundly altered alpha 3 integrin-deficient kidney epithelial cells, such that they converted from a dispersed, elongated morphology to an epithelium-like cobblestone clustering. These results point to novel biochemical and biological functions for tetraspanin palmitoylation.
The Danger Signal S100B Integrates Pathogen– and Danger–Sensing Pathways to Restrain Inflammation

Humans inhale hundreds of Aspergillus conidia without adverse consequences. Powerful protective mechanisms may ensure prompt control of the pathogen and inflammation. Here we reveal a previously unknown mechanism by which the danger molecule S100B integrates pathogen– and danger–sensing pathways to restrain inflammation. Upon forming complexes with TLR2 ligands, S100B inhibited TLR2 via RAGE, through a paracrine epithelial cells/neutrophil circuit that restrained pathogen-induced inflammation. However, upon binding to nucleic acids, S100B activated intracellular TLRs eventually resolve danger-induced inflammation via transcriptional inhibition of S100B. Thus, the spatiotemporal regulation of TLRs and RAGE by S100B provides evidence for an evolving braking circuit in infection whereby an endogenous danger protects against pathogen–induced inflammation and a pathogen–sensing mechanism resolves danger–induced inflammation.
ReviewMicroRNAs : Genomics , Biogenesis , Mechanism , and Function

ulation of hematopoietic lineage differentiation in mammals (Chen et al., 2004), and control of leaf and flower trolled by miRNAs indicate that these examples represent a very small fraction of the total This review highlights what has been learned about MicroRNAs (miRNAs) are endogenous ‫22ف‬ nt RNAs that can play important regulatory roles in animals and miRNAs in the decade since the report of the lin-4 RNA and its regulation of lin-14. The major topics discussed plants by targeting mRNAs for cleavage or transla-tional repression. Although they escaped notice until are miRNA genomics, miRNA biogenesis, miRNA regulatory mechanisms, and the roles of miRNAs in gene regu-relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in latory pathways. multicellular organisms and likely influence the output of many protein-coding genes. Genomics: The miRNA Genes For seven years after the discovery of the lin-4 RNA, the genomics of this type of tiny regulatory RNA appeared In an investigation inspiring for both its perseverance simple: there was no evidence for lin-4-like RNAs be-and its scientific insight, Victor Ambros and colleagues, yond nematodes and no sign of any similar noncoding Rosalind Lee and Rhonda Feinbaum, discovered that RNAs within nematodes. This all changed upon the dis-lin-4, a gene known to control the timing of C. elegans covery that let-7, another gene in the C. elegans hetero-larval development, does not code for a protein but chronic pathway, encoded a second ‫22ف‬ nt regulatory instead produces a pair of small RNAs (Lee et al., 1993). RNA. The let-7 RNA acts to promote the transition from One RNA is approximately 22 nt in length, and the other late-larval to adult cell fates in the same way that the is approximately 61 nt; the longer one was predicted to lin-4 RNA acts earlier in development to promote the fold into a stem loop proposed to be the precursor of progression from the first larval stage to the second the shorter one. The Ambros and Ruvkun labs then no-(Reinhart et al., 2000; Slack et al., 2000). Furthermore, ticed that these lin-4 RNAs had antisense complemen-homologs of the let-7 gene were soon identified in the tarity to multiple sites in the 3Ј UTR of the lin-14 gene human and fly genomes, and let-7 RNA itself was de-This comple-tected in human, Drosophila, and eleven other bilateral mentarity fell in a region of the 3Ј UTR previously pro-animals …
The effect of different immune responses on the evolution of virulent CXCR4–tropic HIV

We use mathematical models to determine possible mechanisms contributing to the evolution and rise of virulent CXCR4–tropic HIV in vivo. The models predict that the ability of the virus to specialize on a given target cell type depends on the exact fitness landscape of the viral mutants. Because this fitness landscape varies between people, this may explain why the evolution of fully CXCR4–tropic strains only occurs in about 50% of infected patients. Assuming that CXCR4–tropic HIV may evolve, we investigate the effect of different immune responses on the rise of such virulent strains. If we assume that CXCR4–tropic HIV is more cytopathic than CCR5–tropic virus, virulent CXCR4–tropic mutants remain suppressed at low levels both in the absence of an immune response, and in the presence of re–sponses that act on the virus before integration into the host genome. On the other hand, this difference in cytopathogenicity is reduced by the presence of immune responses acting on infected cells, allowing CXCR4–tropic HIV to coexist with the CCR5–tropic virus. These results may help to interpret experimental data and are discussed with reference to the literature.
Age-Related Differences in the Attention Network Test (ANT)

This study investigates the effect of aging on alerting, orienting, and conflict resolution by assessing younger (mean age = 25.8) and older (mean age = 67.9) adults' performance in the Attention Network Test that combines, in a single experimental paradigm, a flanker task with alerting and orienting cues. The analyses of response times indicated equivalent orienting and conflict resolution effects in younger and older adults. By contrast, alerting was found to be significantly reduced in the elderly. This result is only marginally in accordance with recent studies addressing the issues of age-related differences in alerting, which provide mixed results. The possible role of methodological differences across studies in accounting for the controversial results concerning the aging affect on alerting is discussed.
General LTL Specification Mining

Temporal properties are useful for describing and reasoning about software behavior, but developers rarely write down temporal specifications of their systems. Prior work on inferring specifications developed tools to extract likely program specifications that fit particular kinds of tool-specific templates. This paper introduces Texada, a new temporal specification mining tool for extracting specifications in linear temporal logic (LTL) of arbitrary length and complexity. Texada takes a userdefined LTL property type template and a log of traces as input and outputs a set of instantiations of the property type (i.e., LTL formulas) that are true on the traces in the log. Texada also supports mining of almost invariants: properties with imperfect confidence. We formally describe Texada’s algorithms and evaluate the tool’s performance and utility.
Delineating the Cardio-Myogenic Hierarchy during Mouse Embryonic Development

The identification of cell surface proteins on stem cells or stem cell derivatives is a key strategy for the functional characterization, isolation, and understanding of stem cell population dynamics. We have turned to cell surface mass spectrometry to increase the candidate pool of membrane proteins on cardiac progenitor cells (CPCs). Specifically, we examined the expression of surface markers on CPCs using an integrated mass spectrometry and microarray-based approach. We analyzed the genome and surface proteome of cardiac progenitors generated from the stagespecific differentiation of mouse (m) and human (h) pluripotent stem cells (PSCs). We have identified and characterized Frizzled 4 (FZD4) as a new marker for lateral plate mesoderm (LPM). We also utilized FZD4 as a marker, in conjunction with fetal liver kinase 1 (FLK1) and platelet derived growth factor alpha (PDGFRA) and demonstrated an increase in CPC purity and a subsequent increase in cardiomyocyte (CM) enrichment. Additionally, we have found FZD4 is also expressed in the hPSC system and results in a similar enrichment in CM. Furthermore, we showed that NORRIN can be presented to the FZD4 receptor to induce Wingless-related integration site (WNT) signaling-mediated proliferation, resulting in an increase in CM output iii from CPCs. This demonstrates the value in knowing the set of surface markers present on a cell at a specific stage of development and the potential to leverage that knowledge into more efficient cell differentiation protocols. Further validation of the function of FZD4 is also being established in a preliminary in vivo study. The identified surface markers also have the potential to isolate cell types not only within the CPC stage, but within the PSC, epiblast, and primitive streak stages as well. These markers have been compiled into a preliminary cell-cell communication network model overlaid with an initial alternative slicing analysis to determine potential mechanisms that impact cell signaling during early CPC development. In summary, the application of a systems biology approach as demonstrated in this thesis, greatly expanded the number of surface markers available and upon further characterization and validation, can improve our understanding of
Vestibular Evoked Myogenic Potential Produced by Bone-Conducted Stimuli: A Study on its Basics and Clinical Applications in Patients with Conductive and Sensorineural Hearing Loss and a Group with Vestibular Schawannoma

Introduction: Vestibular evoked myogenic potential (VEMP) has recently been broadly studied in vestibular disorders. As it is evoked by loud sound stimulation, even mild conductive hearing loss may affect VEMP results. Bone-conducted (BC) stimulus is an alternative stimulation for evoking this response. This study aims to assess the characteristics of BC-VEMP in different groups of patients. Materials and Methods: We performed a cross sectional analysis on 20 healthy volunteers with normal pure-tone audiometry as a control group; and on a group of patients consisted of 20 participants with conductive hearing loss, five with bilateral sensorineural hearing loss and four with vestibular schawannoma. AC and BC-VEMP were performed in all participants. Results: In control group the VEMP responses to both kinds of stimuli had an acceptable morphology and consisted of p13 and n23 waves. Latency value of these main components in each type of stimulus was not significantly different (P>0.05). However, the mean amplitude was larger in BC modality than AC stimulation (P=0.025). In the group with conductive hearing loss, the VEMP response was absent in fifteen (46.87%) of the 32 ears using the AC method, whereas all (100%) displayed positive elicitability of VEMP by BC method. Normal VEMP responses in both stimuli were evoked in all patients with sensorineural hearing loss. In patients with unilateral vestibular schwannomas (VS), 2 (50.00%) had neither AC-VEMP nor BC-VEMP. Conclusion: Auditory stimuli delivered by bone conduction can evoke VEMP response. These responses are of vestibular origin and can be used in vestibular evaluation of patients with conductive hearing loss.
OmniUnpack: Fast, Generic, and Safe Unpacking of Malware

Malicious software (or malware) has become a growing threat as malware writers have learned that signature- based detectors can be easily evaded by "packing" the malicious payload in layers of compression or encryption. State-of-the-art malware detectors have adopted both static and dynamic techniques to recover the pay- load of packed malware, but unfortunately such techniques are highly ineffective. In this paper we propose a new technique, called OmniUnpack, to monitor the execution of a program in real-time and to detect when the program has removed the various layers of packing. OmniUnpack aids malware detection by directly providing to the detector the unpacked malicious payload. Experimental results demonstrate the effectiveness of our approach. OmniUnpack is able to deal with both known and unknown packing algorithms and introduces a low overhead (at most 11% for packed benign programs).
REPRODUCTIVE ISOLATION AND PHYLOGENETIC DIVERGENCE IN NEUROSPORA: COMPARING METHODS OF SPECIES RECOGNITION IN A MODEL EUKARYOTE

Abstract We critically examined methods for recognizing species in the model filamentous fungal genus Neurospora by comparing traditional biological species recognition (BSR) with more comprehensive applications of both BSR and phylogenetic species recognition (PSR). Comprehensive BSR was applied to a set of 73 individuals by performing extensive crossing experiments and delineating biological species based on patterns of reproductive success. Within what were originally considered two species, N. crassa and N. intermedia, we recognized four reproductively isolated biological species. In a concurrent study (Dettman et al. 2003), we used genealogical concordance of four independent nuclear loci to recognize phylogenetic species in Neurospora. Overall, the groups of individuals identified as species were similar whether recognized by reproductive success or by phylogenetic criteria, and increased genetic distance between parents was associated with decreased reproductive success of crosses, suggesting that PSR using genealogical concordance can be used to reliably recognize species in organisms that are not candidates for BSR. In one case, two phylogenetic species were recognized as a single biological species, indicating that significant phylogenetic divergence preceded the development of reproductive isolation. However, multiple biological species were never recognized as a single phylogenetic species. Each of the putative N. crassa × N. intermedia hybrids included in this study was confidently assigned to a single species, using both PSR and BSR. As such, no evidence for a history of hybridization in nature among Neurospora species was observed. By performing reciprocal mating tests, we found that mating type, parental role, and species identity of parental individuals could all influence the reproductive success of matings. We also observed sympatry-associated sexual dysfunction in interspecific crosses, which was consistent with the existence of reinforcement mechanisms.
Visual recognition by counting instances: A multi-instance cardinality potential kernel

Many visual recognition problems can be approached by counting instances. To determine whether an event is present in a long internet video, one could count how many frames seem to contain the activity. Classifying the activity of a group of people can be done by counting the actions of individual people. Encoding these cardinality relationships can reduce sensitivity to clutter, in the form of irrelevant frames or individuals not involved in a group activity. Learned parameters can encode how many instances tend to occur in a class of interest. To this end, this paper develops a powerful and flexible framework to infer any cardinality relation between latent labels in a multi-instance model. Hard or soft cardinality relations can be encoded to tackle diverse levels of ambiguity. Experiments on tasks such as human activity recognition, video event detection, and video summarization demonstrate the effectiveness of using cardinality relations for improving recognition results.
Fatal liver failure associated with pioglitazone

Thiazolidinediones are peroxisomal proliferator activated receptor γ agonists. Troglitazone is associated with idiosyncratic hepatic reaction, liver failure, and death and is withdrawn.1 2 The toxicity of troglitazone is unlikely to be a class effect of thiazolidinediones since rosiglitazone and pioglitazone have shown little evidence of hepatic toxicity.3 Some patients taking pioglitazone, however, have had liver failure, but no deaths are …