Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional and phenotypic comparisons of Ppara knockout and siRNA knockdown mice

RNA interference (RNAi) has great potential as a tool for studying gene function in mammals. However, the specificity and magnitude of the in vivo response to RNAi remains to be fully characterized. A molecular and phenotypic comparison of a genetic knockout mouse and the corresponding knockdown version would help clarify the utility of the RNAi approach. Here, we used hydrodynamic delivery of small interfering RNA (siRNA) to knockdown peroxisome proliferator activated receptor alpha (Ppara), a gene that is central to the regulation of fatty acid metabolism. We found that Ppara knockdown in the liver results in a transcript profile and metabolic phenotype that is comparable to those of Ppara−/− mice. Combining the profiles from mice treated with the PPARα agonist fenofibrate, we confirmed the specificity of the RNAi response and identified candidate genes proximal to PPARα regulation. Ppara knockdown animals developed hypoglycemia and hypertriglyceridemia, phenotypes observed in Ppara−/− mice. In contrast to Ppara−/− mice, fasting was not required to uncover these phenotypes. Together, these data validate the utility of the RNAi approach and suggest that siRNA can be used as a complement to classical knockout technology in gene function studies.
Paleopathology at the Origins of Agriculture: Editor's Summation

In 1982, the Conference on Paleopathology and Socioeconomic Change at the Origins of Agriculture was held in Plattsburgh, New York, to examine previously untested theories about how the adoption of agriculture had impacted human health. The collection of those conference proceedings transformed into this landmark book that set the standard for how to collect, analyse, and interpret osteological data in the study of health transitions. Using skeletal pathologies, the contributors examine how the transition from foraging to farming affected human health and nutrition. Now back in print and for the first time in paperback, Paleopathology at the Origins of Agriculture is a foundational piece in bioarchaeological literature and a central source of information regarding the impact of early farming on socioeconomic evolution. It remains a highly cited reference for archaeologists and physical anthropologists. Contributors present data from nineteen different regions before, during, and after agricultural transitions, analysing populations in Africa, Asia, the Middle East, Europe, and South America while primarily focusing on North America. A wide range of health indicators are discussed, including mortality, episodic stress, physical trauma, degenerative bone conditions, isotopes, and dental pathology.
AHLAT, KIRSAL BÖLGESİNDE GASTRONOMİ TURİZMİNİN MUHTEMEL TOPLUMSAL ETKİLERİ ÜZERİNE NİTEL BİR ÇALIŞMA

Bireylerarasi iliskilerin etkin rol oynadigi ve bu iliskilerin meydana getirdigi etkilesimlerden, bircok disiplinin ortaya ciktigi gorulebilmektedir. Bu disiplinler arasinda kultur ve gelenek uzerinde buyuk bir rolu olan turizm disiplini de yer almaktadir. Turizm, gunumuzde buyuk bir kitlesel ve toplumsal faaliyet olarak kabul edilirken, kendi icerisinde de bircok alternatif turlerini de ortaya cikarmistir. Alternatif turizm faaliyetleri icerisinde onem kazanan alanlardan birisi de, gastronomi turizmi olarak gorulmektedir. Yemek ve yemek kulturunun, turizm ve toplum iliskisi uzerinde ele alinmasi ile onem kazanan gastronomi turizmi, turizm alaninda son yillarda bircok calismaya konu olmaktadir. Bu baglamda calismanin amaci, kirsal turizm bolgelerinde gerceklesen gastronomi turizminin meydana getirdigi toplumsal etkileri ortaya koyabilmektir. Calismada, nitel arastirma yaklasimlarindan yuz yuze gorusme yontemi kullanilmistir. Veriler, 2012 yili Agustos ayinda Bitlis ilinin Ahlat ilcesinde ikamet eden yerli halk ile yapilan yuz yuze gorusmeler neticesinde toplanmistir. Gorusme yontemiyle elde edilen verilerin analizinde betimleyici analiz teknigi kullanilmistir.
Environmental and Social Factors Influencing the Price of Land in Southwestern Virginia, USA, 1786–1830

Abstract Topographically isolated communities of the southern Appalachian Mountains provide an ideal area in which to examine the impact of environmental and social connections on the economy of land sales. Our objective was to identify whether the price of land in a small Appalachian county of southwestern Virginia, USA, from 1786 to 1830, was influenced by area, month or year of sale, water availability, presence of tree species that were proxies of site quality, grantor/grantee residency, or familial relationship between grantor and grantee. The multiple regression model identified four significant factors that influenced the price of land during early European settlement of the southern Appalachian Mountains. Larger areas of land sold for lower prices. Landowners sold land to relatives at a lower price than to nonrelatives. The presence of surface water or red maple (Acer rubrum) on the property was associated with lower land prices. The negative relationship between water and price of land was likely a reflection that the parcels sold at the highest prices were in towns where streams or rivers were no longer relied upon as a water source. The model explained 39% of the variation and demonstrated a blend of environmental and social factors that influenced land sale patterns during early European settlement of the Appalachian Mountains.
The Dna Helicase Pfh1 Promotes Fork Merging at Replication Termination Sites to Ensure Genome Stability

Bi-directionally moving DNA replication forks merge at termination sites composed of accidental or programmed DNA-protein barriers. If merging fails then regions of unreplicated DNA can result in the breakage of DNA during mitosis, which in turn can give rise to genome instability. Despite its importance little is known about the mechanisms that promote the final stages of fork merging in eukaryotes. Here we show that the Pif1 family DNA helicase Pfh1 plays a dual role in promoting replication fork termination. Firstly it faciltates replication past protein-DNA barriers and secondly it promotes the merging of replication forks. A failure of these processes in Pfh1 deficient cells results in aberrant chromosome segregation and heightened genome instability.
Practical Online Network Stack Evolution

Protocol stacks can optimize their performance well for pre-defined environments and are usually hand-engineered in advance: This means that adding new protocols or drastically changing the run-time system or assumed traffic patterns would require re-engineering. As an alternative we present an autonomous stack composition framework inspired by biological evolution: Compositions compete online and new compositions evolve from the best previous performers. We demonstrate the feasibility of our runtime adaptive approach and show through simulations that it can find efficient solutions where offline approaches fail.
An evaluation method of a micro-arrayed multispectral filter mosaic

In recent decades, multispectral imaging (MSI) has been approved as an effective tool to detect and discriminate targets in industrial application. A narrowband micro-arrayed multispectral filter mosaic (MSFM) based on MSI technology is proposed to miniaturize MSI instrumentation. There are many reasons to believe that this innovation is going to replace the traditional methods of filtering or dispersing light and bring MSI applications to more industrial fields. However, highly integrated micro pieces of MSFM are arranged periodically, and the spectral profiles of two adjacent pieces cause a spectral interference (SI). To express and estimate the extent of SI, an evaluation method is proposed and its feasibility is reported in this paper. Additionally, the ways reducing the extent of SI are suggested.
Conserved sequence motifs among bacterial, eukaryotic, and archaeal phosphatases that define a new phosphohydrolase superfamily

Members of a new molecular family of bacterial nonspecific acid phosphatases (NSAPs), indicated as class C, were found to share significant sequence similarities to bacterial class B NSAPs and to some plant acid phosphatases, representing the first example of a family of bacterial NSAPs that has a relatively close eukaryotic counterpart. Despite the lack of an overall similarity, conserved sequence motifs were also identified among the above enzyme families (class B and class C bacterial NSAPs, and related plant phosphatases) and several other families of phosphohydrolases, including bacterial phosphoglycolate phosphatases, histidinol‐phosphatase domains of the bacterial bifunctional enzymes imidazole‐glycerolphosphate dehydratases, and bacterial, eukaryotic, and archaeal phosphoserine phosphatases and threalose‐6‐phosphatases. These conserved motifs are clustered within two domains, separated by a variable spacer region, according to the pattern [FILMAVT]‐D‐[ILFRMVY]‐D‐[GSNDE]‐[TV]‐[ILVAM]‐[ATS VILMC]‐X‐{YFWHKR}‐X‐{YFWHNQ}‐X( 102, 191 )‐{KRHNQ}‐G‐D‐{FYWHILVMC}‐{QNH}‐{FWYGP}‐D‐{PSNQYW}. The dephosphorylating activity common to all these proteins supports the definition of this phosphatase motif and the inclusion of these enzymes into a superfamily of phosphohydrolases that we propose to indicate as “DDDD” after the presence of the four invariant aspartate residues. Database searches retrieved various hypothetical proteins of unknown function containing this or similar motifs, for which a phosphohydrolase activity could be hypothesized.
Cell-Permeable Peptide Inhibitors of JNK: Novel Blockers of β-Cell Death

Stress conditions and proinflammatory cytokines activate the c-Jun NH2-terminal kinase (JNK), a member of the stress-activated group of mitogen-activated protein kinases (MAPKs). We recently demonstrated that inhibition of JNK signaling with the use of the islet-brain (IB) 1 and 2 proteins prevented interleukin (IL)-1β—induced pancreatic β-cell death. Bioactive cell-permeable peptide inhibitors of JNK were engineered by linking the minimal 20-amino acid inhibitory domains of the IB proteins to the 10-amino acid HIV-TAT sequence that rapidly translocates inside cells. Kinase assays indicate that the inhibitors block activation of the transcription factor c-Jun by JNK. Addition of the peptides to the insulin-secreting βTC-3 cell line results in a marked inhibition of IL-1β—induced c-jun and c-fos expression. The peptides protect βTC-3 cells against apoptosis induced by IL-1β. All-D retro-inverso peptides penetrate cells as efficiently as the L-enantiomers, decrease c-Jun activation by JNK, and remain highly stable inside cells. These latter peptides confer full protection against IL-1β—induced apoptosis for up to 2 weeks of continual treatment with IL-1β. These data establish these bioactive cell-permeable peptides as potent pharmacological compounds that decrease intracellular JNK signaling and confer long-term protection to pancreatic β-cells from IL-1β—induced apoptosis.
Triclabendazole Effect on Protease Enzyme Activity in the Excretory- Secretory Products of Fasciola hepatica in Vitro

Background Fasciola hepatica is one of the most important helminthes parasites and triclabendazole (TCBZ) is routinely used for treatment of infected people and animals. Secreted protease enzymes by the F. hepatica plays a critical role in the invasion, migration, nutrition and the survival of parasite and are key targets for novel drugs and vaccines. The aim of study was to determine the protease activity of excretory- secretory products (ESP) of F. hepatica in the presence of TCBZ anthelmintic. Methods F. hepatica helminthes were collected and cultured within RPMI 1640 [TCBZ treated (test) and untreated (control)] for 6 h at 37 °C. ESP of treated and control were collected, centrifuged and supernatants were stored at -20°C. Protein concentrations were measured according to Bradford method. Protease enzymes activities of ESP samples were estimated by using sigma’s non-specific protease activity assay. ESP protein bands were detected by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Results Mean protein concentrations in control and treated of ESP samples were determined 196.1 ±14.52 and 376.4 ±28.20 μg/ml, respectively. Mean protease enzymes activities in control and treated were 0.37 ±0.1 and 0.089 ±0.03 U/ml, respectively. Significant difference between proteins concentrations and protease enzymes activities of two groups was observed (P<0.05). SDS-PAGE showed different patterns of protein bands between treated and control samples. Conclusion The TCBZ reduced secreted protease enzymes activities and possibly effects on invasion, migration, nutrition and particularly survival of the parasite in the host tissues.
Implementing Parallel LU Factorization with Pipelining on a MultiCore Using OpenMP

Recent developments in high performance computer architecture have a significant effect on all fields of scientific computing. Linear algebra and especially the solution of linear systems of equations lies at the heart of many applications in scientific computing. This paper describes and analyzes three parallel versions of the dense LU factorization method that is used in linear system solving on a multicore using OpenMP interface. More specifically, we present two naive parallel algorithms based on row block and row cyclic data distribution and we put special emphasis on presenting a third parallel algorithm based on the pipeline technique. Further, we propose an implementation of the pipelining technique in OpenMP. Experimental results on a multicore CPU show that the proposed OpenMP pipeline implementation achieves good overall performance compared to the other two naive parallel methods. Finally, in this work we propose a simple, fast and reasonably analytical model to predict the performance of the LU decomposition method with the pipelining technique.
Synergy between PI3K/Akt and Raf/MEK/ERK Pathways in IGF-1R Mediated Cell Cycle Progression and Prevention of Apoptosis in Hematopoietic Cells

The insulin like growth factor-1 (IGF-1) receptor (R) induced PI3K/Akt signal transduction cascade has critical roles in prevention of apoptosis and regulation of cell cycle progression. Here, we discuss the effects of IGF-1R-mediated signal transduction on hematopoietic cells which normally require interleukin-3 (IL-3) for growth and prevention of apoptosis. Cytokine-dependent FDC-P1 hematopoietic cells were conditionally transformed to grow in response to overexpression of IGF-1R in the presence of IGF-1. When these cells were deprived of IL-3 or IGF-1 for 24 hrs, they exited the cell cycle, activated caspase 3 and underwent apoptosis. The effects of inhibitors which targeted the PI3K/Akt and Raf/MEK/ERK pathways were determined. When the cells were cultured with IGF-1 and either PI3K or MEK inhibitors, cell cycle progression and DNA synthesis were inhibited and caspase 3 activity and apoptosis were induced. Co-inhibition of both pathways synergized to prevent cell cycle progression, inhibit DNA synthesis and induce apoptosis. These inhibitors had more apoptotic inducing effects when the cells were grown in response to IGF-1 than IL-3, indicating that IL-3 can induce additional anti-apoptotic pathways. These results demonstrate that the PI3K/Akt and Raf/MEK/ERK pathways are intimately involved in IGF-1R-mediated cell cycle progression and prevention of apoptosis in hematopoietic cells.
User Behaviors in Related Word Retrieval and New Word Detection: A Collaborative Perspective

Nowadays, user behavior analysis and collaborative filtering have drawn a large body of research in the machine learning community. The goal is either to enhance the user experience or discover useful information hidden in the data. In this article, we conduct extensive experiments on a Chinese input method data set, which keeps the word lists that users have used. Then, from the collaborative perspective, we aim to solve two tasks in natural language processing, that is, related word retrieval and new word detection. Motivated by the observation that two words are usually highly related to each other if they co-occur frequently in users’ records, we propose a novel semantic relatedness measure between words that takes both user behaviors and collaborative filtering into consideration. We utilize this measure to perform related word retrieval and new word detection tasks. Experimental results on both tasks indicate the applicability and effectiveness of our method.
Ozone production in urban plumes transported over water: Photochemical model and case studies in the northeastern and midwestern United States

Abnormally high concentrations of O3 have been observed in rural locations on the shore of Lake Michigan and on the Atlantic coast in Maine, at a distance of 300 km or more from major anthropogenic sources. We hypothesize that this O3 is associated with transport from major urban centers and with the suppression of vertical mixing as urban plumes are transported over water. A dynamical/photochemical model is developed that represents formation of O3 in shoreline environments and is used to simulate case studies for Lake Michigan and the northeastern United States. Results suggest that a broad region with elevated O3, NOx and volatile organic carbon (VOC) forms as the Chicago plume travels over Lake Michigan, a pattern consistent with observed O3 at surface monitoring sites. Near-total suppression of dry deposition of O3 and NOx over the lake is needed to produce high O3. Results for the east coast suggest that the observed peak O3 can only be reproduced by a model that includes suppressed vertical mixing and deposition over water, 2-day transport of a plume from New York, and superposition of the New York and Boston plumes. An investigation of the sensitivity of O3 to emissions of NOx and VOC suggests that results vary greatly between cities, even when the composition of urban emissions is similar. An index for VOC versus NOx sensitivity is shown to correlate with total reactive nitrogen (NOy) at the time of peak O3.
Benefits of building wireless sensor networks on commodity hardware and software stacks

The majority of wireless sensor networks are built on bespoke platforms, that is, custom designed and built hardware with a light weight software stack. There are a number of advantages to this approach. First, the ability to closely match and minimise the resource requirements (e.g., power consumption and communications protocols) to those that are suitable for the intended deployment. Second, as an entire hardware and software stack is often designed or at least optimised for each deployment, the latest advances can be quickly incorporated. However, this model generally requires the expertise of hardware and software engineers to design and build the system. In turn, this increases the cost and tends to shift the focus away from the initial science towards the development of the wireless sensor networks. This paper explores the utility and practicality of building wireless sensor networks based on commercially available embedded single board computing platforms using standard consumer operating systems. Our test bed was built using Gumstix computing platform, running a Linux Operating System (OS) with a java-based middleware coupled to low-cost scientific grade sensors. Test deployments have found this to be a highly versatile solution, able to leverage the flexibility of commodity hardware and software while maintaining reasonable utility.
HIV-1-Specific Antibody Response and Function after DNA Prime and Recombinant Adenovirus 5 Boost HIV Vaccine in HIV-Infected Subjects

Little is known about the humoral immune response against DNA prime-recombinant adenovirus 5 (rAd5) boost HIV vaccine among HIV-infected patients on long-term suppressive antiretroviral therapy (ART). Previous studies emphasized cellular immune responses; however, current research suggests both cellular and humoral responses are likely required for a successful therapeutic vaccine. Thus, we aimed to understand antibody response and function induced by vaccination of ART-treated HIV-1-infected patients with immune recovery. All subjects participated in EraMune 02, an open-label randomized clinical trial of ART intensification followed by a six plasmid DNA prime (envA, envB, envC, gagB, polB, nefB) and rAd5 boost HIV vaccine with matching inserts. Antibody binding levels were determined with a recently developed microarray approach. We also analyzed neutralization efficiency and antibody-dependent cellular cytotoxicity (ADCC). We found that the DNA prime-rAd5 boost vaccine induced a significant cross-clade HIV-specific antibody response, which correlated with antibody neutralization efficiency. However, despite the increase in antibody binding levels, the vaccine did not significantly stimulate neutralization or ADCC responses. This finding was also reflected by a lack of change in total CD4+ cell associated HIV DNA in those who received the vaccine. Our results have important implications for further therapeutic vaccine design and administration, especially in HIV-1 infected patients, as boosting of preexisting antibody responses are unlikely to lead to clearance of latent proviruses in the HIV reservoir.
Differences in the aromatic domain of homologous streptococcal fibronectin‐binding proteins trigger different cell invasion mechanisms and survival rates

Group A streptococci (GAS, Streptococcus pyogenes) and Group G streptococci (GGS, Streptococcus dysgalactiae ssp. equisimilis) adhere to and invade host cells by binding to fibronectin. The fibronectin‐binding protein SfbI from GAS acts as an invasin by using a caveolae‐mediated mechanism. In the present study we have identified a fibronectin‐binding protein, GfbA, from GGS, which functions as an adhesin and invasin. Although there is a high degree of similarity in the C‐terminal sequence of SfbI and GfbA, the invasion mechanisms are different. Unlike caveolae‐mediated invasion by SfbI‐expressing GAS, the GfbA‐expressing GGS isolate trigger cytoskeleton rearrangements. Heterologous expression of GfbA on the surface of a commensal Streptococcus gordonii and purified recombinant protein also triggered actin rearrangements. Expression of a truncated GfbA (lacking the aromatic domain) and chimeric GfbA/SfbI protein (replacing the aromatic domain of SfbI with the GfbA aromatic domain) on S. gordonii or recombinant proteins alone showed that the aromatic domain of GfbA is responsible for different invasion mechanisms. This is the first evidence for a biological function of the aromatic domain of fibronectin‐binding proteins. Furthermore, we show that streptococci invading via cytoskeleton rearrangements and intracellular trafficking along the classical endocytic pathway are less persistence than streptococci entering via caveolae.
Diviner Lunar Radiometer Experiment: Early Mapping Mission Results

Paige, B. T. Greenhagen, A. R. Vasavada, C. Allen, J. L Bandfield, N. E Bowles, S. B Calcutt, E. M. De Jong, R. C. Elphic, E. J Foote, M. C. Foote, K. L Donaldson Hanna, D. J. McCleese, R. R Ghent, T. D. Glotch, P O. Hayne, P. G. Lucey, B. C. Murray, J. T. Schofield, M. A. Siegler, K. Snook, L. A. Soderblom, E. Song, F. W. Taylor, I. R. Thomas, M. B. Wyatt, University of California, Los Angeles, Department of Earth and Space Sciences, 595 Charles Young Drive East, Los Angeles, CA 90095, dap@moon.ucla. edu JPL/Caltech, NASA JSC, U. Washington, Oxford Univ., NASA Ames, Brown Univ., U. Toronto, Sony Brook Univ., U. Hawaii, Caltech, NASA GSFC, USGS, Flagstaff.