Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors Affecting Clove Exports in North Sumatera Province

This study aims to analyze the effect of production, the population of the destination country, the GDP of the destination country, the distance between the Province of North Sumatra and the destination country, and the exchange rate of the export destination country in US $ to the value of clove export in North Sumatra Province 2011-2015 based on gravity model in the countries of Singapore, Malaysia, Vietnam, United States, India, United Kingdom, and Taiwan. Data analysis method used is panel data regression analysis with Random Effect Model. The results of this study indicate that the production of cloves and Gross Domestic Product of export destination countries has a positive and significant influence, the distance between North Sumatra Province and export destination countries has a negative and significant effect on the value of clove exports in North Sumatra Province. While the number of population of export destination countries showed a positive and insignificant influence, the nominal exchange rate of export destination countries had negative and insignificant effect on clove export value in North Sumatera Province.
Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

During transcription elongation, RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis. Under this assumption, recent single-molecule studies proposed a branched Brownian ratchet mechanism that necessitates a putative secondary nucleotide binding site on the enzyme. By challenging individual yeast RNA polymerase II with a nucleosomal barrier, we separately measured the forward and reverse translocation rates. Surprisingly, we found that the forward translocation rate is comparable to the catalysis rate. This finding reveals a linear, non-branched ratchet mechanism for the nucleotide addition cycle in which translocation is one of the rate-limiting steps. We further determined all the major on- and off-pathway kinetic parameters in the elongation cycle. The resulting translocation energy landscape shows that the off-pathway states are favored thermodynamically but not kinetically over the on-pathway states, conferring the enzyme its propensity to pause and furnishing the physical basis for transcriptional regulation. DOI: http://dx.doi. org/10.7554/eLife.00971. 001
Lhx1 maintains synchrony among circadian oscillator neurons of the SCN

The robustness and limited plasticity of the master circadian clock in the suprachiasmatic nucleus (SCN) is attributed to strong intercellular communication among its constituent neurons. However, factors that specify this characteristic feature of the SCN are unknown. Here, we identified Lhx1 as a regulator of SCN coupling. A phase-shifting light pulse causes acute reduction in Lhx1 expression and of its target genes that participate in SCN coupling. Mice lacking Lhx1 in the SCN have intact circadian oscillators, but reduced levels of coupling factors. Consequently, the mice rapidly phase shift under a jet lag paradigm and their behavior rhythms gradually deteriorate under constant condition. Ex vivo recordings of the SCN from these mice showed rapid desynchronization of unit oscillators. Therefore, by regulating expression of genes mediating intercellular communication, Lhx1 imparts synchrony among SCN neurons and ensures consolidated rhythms of activity and rest that is resistant to photic noise. DOI: http://dx.doi. org/10.7554/eLife.03357. 001
Efficient selection of transgenic mouse embryos using EGFP as a marker gene

We have established a reliable method that uses the EGFP (Enhanced Green Fluorescent Protein) gene as a marker for selecting transgenic embryos from preimplantation embryos. Embryos that were subjected to the pronuclear microinjection of the CMV/β‐actin/EGFP fusion gene were cultured in vitro until they developed into the morulae‐ or blastocyst‐stage. The expression of EGFP was easily observed by a fluorescent microscopy. There appeared to be no damage to the in vivo developmental ability of the embryos in response to the EGFP excitation light, which utilized an IB filter for a period of 30 min. Modified PCR analysis using Dpn I and Bal 31 digestion of the embryonic DNA showed that all of the embryos expressing EGFP in all their cells were transgenic, while more than half with mosaic expression of EGFP were not transgenic. Approximately 77% of pups born from the embryos that uniformly expressed the EGFP gene were transgenic, while 21.4% of pups from the embryos with mosaic expression were transgenics. The results showed that the use of EGFP as a marker is very useful and reliable for selecting transgenic embryos, and that it is important to transfer the embryos expressing EGFP in all their cells to obtain truly transgenic animals. Mol. Reprod. Dev. 54:43–48, 1999. © 1999 Wiley‐Liss, Inc.
Characterization and Low-Dimensional Modeling of Urban Fluid Flow

Abstract : This report describes work studying the structure of a model urban boundary layer flow. The flow around this geometry was studied both experimentally as well as computationally. For the experiment, a Stereoscopic Particle Image Velocimetry (SPIV) method was developed that allows for a three-dimensional description of this urban flow. On the computational side, a new spectral-element code was developed that was demonstrated to produce accurate results, and can scale to thousands of processors on large high-performance computing systems. Wind tunnel experiments were performed at a number of different angles of incidence, providing for the first time a detailed overview of the effect of wind direction on the flow structure. The effects of incidence angles from 0 to 45 degrees of the incoming flow with respect to the urban array were investigated. A strong channeling effect is observed for all incidence angles and is in agreement with that observed in other investigations for as little as 4 degrees. This channeling significantly affects the turbulence distribution within the array, the correlations between the various gust components and the structures responsible for contaminant transport.
CEO Compensation and Incentives - Evidence from M&A Bonuses

We investigate CEO compensation for completing M&A deals. 39% of the acquiring firms in our sample state that they compensate their CEOs for completing the deal, and that the compensation comes mainly in the form of a cash bonus. We find that CEOs who have more power to influence board decisions receive significantly larger bonuses. We also find a positive relation between bonus compensation and measures of effort, but not between bonus compensation and deal performance. CEOs with more power also tend to engage in larger deals relative to the size of their own firms, and the market responds more negatively to their acquisition announcements. Our evidence is consistent with the argument that managerial power is the primary driver of M&A bonuses.
Assessment of Methodological Quality of Economic Evaluations in Belgian Drug Reimbursement Applications

Objectives This paper aims to assess the methodological quality of economic evaluations included in Belgian reimbursement applications for Class 1 drugs. Materials and Methods For 19 reimbursement applications submitted during 2011 and Spring 2012, a descriptive analysis assessed the methodological quality of the economic evaluation, evaluated the assessment of that economic evaluation by the Drug Reimbursement Committee and the response to that assessment by the company. Compliance with methodological guidelines issued by the Belgian Healthcare Knowledge Centre was assessed using a detailed checklist of 23 methodological items. The rate of compliance was calculated based on the number of economic evaluations for which the item was applicable. Results Economic evaluations tended to comply with guidelines regarding perspective, target population, subgroup analyses, comparator, use of comparative clinical data and final outcome measures, calculation of costs, incremental analysis, discounting and time horizon. However, more attention needs to be paid to the description of limitations of indirect comparisons, the choice of an appropriate analytic technique, the expression of unit costs in values for the current year, the estimation and valuation of outcomes, the presentation of results of sensitivity analyses, and testing the face validity of model inputs and outputs. Also, a large variation was observed in the scope and depth of the quality assessment by the Drug Reimbursement Committee. Conclusions Although general guidelines exist, pharmaceutical companies and the Drug Reimbursement Committee would benefit from the existence of a more detailed checklist of methodological items that need to be reported in an economic evaluation.
The relationship between SMN, the spinal muscular atrophy protein, and nuclear coiled bodies in differentiated tissues and cultured cells.

The spinal muscular atrophy protein, SMN, is a cytoplasmic protein that is also found in distinct nuclear structures called "gems. " Gems are closely associated with nuclear coiled bodies and both may have a direct role in snRNP maturation and pre-RNA splicing. There has been some controversy over whether gems and coiled bodies colocalize or form adjacent/independent structures in HeLa and other cultured cells. Using a new panel of antibodies against SMN and antibodies against coilin-p80, a systematic and quantitative study of adult differentiated tissues has shown that gems always colocalize with coiled bodies. In some tissues, a small proportion of coiled bodies (<10%) had no SMN, but independent or adjacent gems were not found. The most striking observation, however, was that many cell types appear to have neither gems nor coiled bodies (e.g., cardiac and smooth muscle, blood vessels, stomach, and spleen) and this expression pattern is conserved across human, rabbit, and pig species. This shows that assembly of distinct nuclear bodies is not essential for RNA splicing and supports the view that they may be storage sites for reserves of essential proteins and snRNPs. Overexpression of SMN in COS-7 cells produced supernumerary nuclear bodies, most of which also contained coilin-p80, confirming the close relationship between gems and coiled bodies. However, when SMN is reduced to very low levels in type I SMA fibroblasts, coiled bodies are still formed. Overall, the data suggest that gem/coiled body formation is not determined by high cytoplasmic SMN concentrations or high metabolic activity alone and that a differentiation-specific factor may control their formation.
Comparative Study of VaginalLactobacillus Phages Isolated from Women in the United States and Turkey: Prevalence, Morphology, Host Range, and DNA Homology

ABSTRACT Lactobacilli play an important role in maintaining vaginal health. However, during bacterial vaginosis lactobacilli decrease for unknown reasons. Our preliminary study showed that phages could infect vaginal lactobacilli. Therefore, the aim of this study was to analyze the distribution, virulence, and types of vaginal Lactobacillusphages isolated from women of two countries: the United States and Turkey. A total of 209 vaginal lactobacilli were isolated from reproductive-aged women in the United States (n = 107) and Turkey (n = 102). By analysis of 16S rRNA gene sequence and by comparison of protein profiles, most lactobacilli were identified as L. crispatus, L. gasseri, andL. jensenii. After mitomycin C induction, 28% of American lactobacilli and 36% of Turkish lactobacilli released phages. A total of 67 phages were isolated and further characterized by their host range, electron microscopy, and DNA homology. All 67 phages were infective against lactobacilli from both collections. The host ranges of most phages were broad, including multiple Lactobacillusspecies. Even though the phages were all temperate, they were able to cause lytic infection in various strains. The electron micrographs of these phages showed a hexagon-shaped head and a long tail with or without a contractile tail sheath. Based on their morphology, these phages belonged to Bradley's phage groups A and B, and could be further classified into four morphotypes. All four types were found among American phages, but only three were found among Turkish isolates. DNA hybridization with labeled probes of the four types of phages revealed that additional genetic types existed within each morphotype among these phages. The phage genomic sizes ranged between 34 and 55 kb. Many of the lysogenic Lactobacillus strains released phages spontaneously at a high frequency of 10−3to 10−4 PFU/cell. In conclusion, lysogeny in vaginal lactobacilli is widely spread. Some lysogenic lactobacilli spontaneously release phages with a broad host range, which can be lytic against other vaginal lactobacilli regardless of their geographic origin.
Successful optimization of CRISPR/Cas9-mediated defined point mutation knock-in using allele-specific PCR assays in zebrafish

Single-stranded oligodeoxynucleotides (ssODN) are donor templates for homology-directed repair-based knock-in of point mutations using CRISPR/Cas9. To optimize the efficiency of ssODN-based knock-ins in zebrafish, we developed allele-specific PCR (AS-PCR) assays for introducing point mutations in tp53, cdh5 and lmna as case studies. In these point mutation strategies we introduced the codon mutations, sgRNA site mutations and restriction sites which can be detected by AS-PCR with the primers matching their respective alleles in combination with a common primer. We employed the anti-sense asymmetric oligo design as the main optimization as well as phosphorothioate oligo modification and also observed that proximity of the mutation site to the Cas9 cut site improves the efficiency when knock-ins into different genes were compared. We improved the efficiencies of two tp53 knock-ins using anti-sense asymmetric ultramer oligos (126-nt in length with homology arms of 36 and 90 nucleotides, anti-sense to the sgRNA) by 3-10 fold, the optimizations which resulted in successful founders for both tp53 knock-ins with transmission rates of 20-40 %. The initially low knock-in efficiency for tp53 mutants was likely due to the distance between the Cas9 cut site and mutations since cdh5 G767S knock-in located at the cut site had much higher founder identification and germline transmission rates. The phosphorothioate oligo modifications was used for a lamin A/C (lmna) knock-in strategy and it resulted in 40 % overall improvement in knock-in efficiency and greater knock-in consistency. We also determined that AS-PCR detected false-positive knock-ins which constituted 25-80 % of total in different strategies and developed a workflow to screen out the founders and F1 zebrafish carrying these undesirable modifications. In summary, we provide a complementary set of optimizations for CRISPR/Cas9-based ssODN knock-ins in zebrafish using a novel combination of methods.
The Human Organization

The Human Organization is a response to the network morphology. As networks supersede hierarchy as the predominant form of organization, fluid processes and flexible teams need to replace fixed reporting lines and familiar functions. The barriers to achieving this are more often cultural and emotional than they are commercial and technological. This paper proposes that effective knowledge‐based businesses will be built on human network connections. This requires much greater investment in social processes of integration and in our individual ability to connect with each other. Without this human agenda, the openness and learning on which the generative knowledge‐based environment depends will remain beyond our reach, together with our ability to work and transfer knowledge across complex and shifting organizational boundaries.
Parallel algorithms for personalized communication and sorting with an experimental study (extended abstract)

A fundamental challenge for parallel computing is to obtain high-level, architecture independent, algorithms which execute efficiently on general-purpose parallel machines. With the emergence of message passing standards such as MPI, it has become easier to design efficient and portable parallel algorithms by making use of these communication primitives. While existing primitives allow an assortment of collective communication routines, they do not handle an important communication event when most or all processors have nonuniformly sized personalized messages to exchange with each other. We first present an algorithm for the h-relation personalized communication whose efficient implementation will allow high performance implementations of a large class of algorithms. We then consider how to effectively use these communication primitives to address the problem of sorting. Previous schemes for sorting on general-purpose parallel machines have had to choose between poor load balancing and irregular communication or multiple rounds of all-to-all personalized communication. In this paper, we introduce a novel variation on sample sort which uses only two rounds of regular all-to-all personalized communication in a scheme that yields very good load balancing with virtually no overhead. Another variation using regular sampling for choosing the splitters has similar performance with deterministic guaranteed bounds on the memory and communication requirements. Both of these variations efficiently handle the presence of duplicates without the overhead of tagging each element. The personalized communication and sorting algorithms presented in this paper have been coded in SPLIT-C and run on a variety of platforms, including the Thinking Machines CM-5, IBM SP-2, Gray Research T3D, Meiko Scientific CS-2, and the Intel Paragon. Our experimental results are consistent with the theoretical analyses and illustrate “ The support by NASA Graduate Student Researcher Fellowship No NGT-50951 is gratefully acknowledged tsupported in part by NSF grant No cCR-91113135 and NSF HPCC/GCAG grant No. BIR-9318183, Permission to make digital/bard copies of all or part of this material for personal or classroom use is granted without fee provided that the copies are not made or $stributed for profit or commercial advantage, tbe copyn,ght notice, the . Utle,of the publication and Its date appear, and notice is given that copymght M by pernmwon of the ACM, Inc. To copy otherwise, to republish, to post on servers or to redistribute to Iista, requires specific permission and/or fee. SPAA’96, Padua, Italy 01996 ACM 0-89791-809-6/96/06 . $3.50 the scalability and efficiency of our algorithms across different platforms. In fact, they seem to outperform all similar algorithms known to the authors on these platforms, ancl performance is invariant over the set of input distributions unlike previous efficient algorithms. Our sorting results also compare favorably with those reported for the simpler ranking problem posed by the NAS Integer Sorting ( 1S) Benchmark.
Factors influencing satisfaction and loyalty in online shopping: an integrated model

Purpose – Taking into consideration external (technology acceptance factors, website service quality) as well as internal (specific holdup cost) factors, this paper aims to explore how internet customer satisfaction and loyalty can be associated with each other and how they are affected by these dynamics.Design/methodology/approach – This study adopts structural equation modelling (SEM) as the main analytical tool. It investigates the shopping experiences of users of the major shopping websites of Taiwan.Findings – The research results point to the following: first, customer e‐satisfaction will positively influence customer e‐loyalty directly; second, technology acceptance factors will positively influence customer e‐satisfaction and e‐loyalty directly; third, website service quality can positively influence customer e‐satisfaction and e‐loyalty directly; and fourth, specific holdup cost can positively influence customer e‐loyalty directly, but cannot positively influence customer e‐satisfaction directly.
SemEval-2007 Task 02: Evaluating Word Sense Induction and Discrimination Systems

The goal of this task is to allow for comparison across sense-induction and discrimination systems, and also to compare these systems to other supervised and knowledge-based systems. In total there were 6 participating systems. We reused the SemEval-2007 English lexical sample subtask of task 17, and set up both clustering-style unsupervised evaluation (using OntoNotes senses as gold-standard) and a supervised evaluation (using the part of the dataset for mapping). We provide a comparison to the results of the systems participating in the lexical sample subtask of task 17.
Critical indirect effects of climate change on sub-Antarctic ecosystem functioning

Sub-Antarctic islands represent critical breeding habitats for land-based top predators that dominate Southern Ocean food webs. Reproduction and molting incur high energetic demands that are sustained at the sub-Antarctic Prince Edward Islands (PEIs) by both inshore (phytoplankton blooms; “island mass effect”; autochthonous) and offshore (allochthonous) productivity. As the relative contributions of these sustenance pathways are, in turn, affected by oceanographic conditions around the PEIs, we address the consequences of climatically driven changes in the physical environment on this island ecosystem. We show that there has been a measurable long-term shift in the carbon isotope signatures of the benthos inhabiting the shallow shelf region of the PEIs, most likely reflecting a long-term decline in enhanced phytoplankton productivity at the islands in response to a climate-driven shift in the position of the sub-Antarctic Front. Our results indicate that regional climate change has affected the balance between allochthonous and autochthonous productivity at the PEIs. Over the last three decades, inshore-feeding top predators at the islands have shown a marked decrease in their population sizes. Conversely, population sizes of offshore-feeding predators that forage over great distances from the islands have remained stable or increased, with one exception. Population decline of predators that rely heavily on organisms inhabiting the inshore region strongly suggest changes in prey availability, which are likely driven by factors such as fisheries impacts on some prey populations and shifts in competitive interactions among predators. In addition to these local factors, our analysis indicates that changes in prey availability may also result indirectly through regional climate change effects on the islands' marine ecosystem. Most importantly, our results indicate that a fundamental shift in the balance between allochthonous and autochthonous trophic pathways within this island ecosystem may be detected throughout the food web, demonstrating that the most powerful effects of climate change on marine systems may be indirect.