Miracle-dz/UniFAR-FTUs huggingface dataset:
Hematological, serum, and plasma chemical constituents in pantropical spotted dolphins (Stenella attenuata) following chase, encirclement, and tagging

Hematology, serum chemistry, and plasma hormones were evaluated in 72 pantropical spotted dolphins (Stenella attenuata attenuata) from the eastern tropical Pacific in an attempt to define the degree of stress associated with chase and encirclement by a tuna purse seiner, and are here reported for the first time for this species. Dolphins had high levels of dopamine and moderately elevated levels of enzymes indicative of the expected muscle damage following exertion of the chase. The length of time between the start of the capture operation and blood sampling correlated with increases in platelet and white blood cell counts and mean cell hemoglobin concentration, while the length of time between net tie-down and blood sampling influenced platelet, white blood cell, and eosinophil counts. Ten dolphins recaptured 1–3 d after their first capture had significantly lower serum creatinine kinase, thyroid (T4) and globulin levels compared to values in dolphins sampled at nominal first capture. Although small sample sizes and large individual variation limit interpretation, these data indicate a stress response occurred in all dolphins, but the extent of the response is within the expected range for adaptive responses previously measured in limited numbers of wild mammals.
Route Optimization of Stacker in Automatic Warehouse Based on Genetic Algorithm

Today, automatic warehouse system gradually replaced manual labor, and played an important role in the production work, especially in the cargo handling work. It was important to research the time-consuming and efficiency of stacker in the automated warehouse system. This paper researched the path of stacker in automated warehouse and calculated the operation time of stacker working path according to actual working condition, and then put forward a route optimization method of stacker based on genetic algorithm, finally simulated this algorithm by using MATLAB. The simulation results showed that this algorithm could shorten the way of stacker, and increase the working efficiency of the warehouse. DOI: http://dx.doi. org/10.11591/telkomnika.v11i11. 2959 Full Text: PDF
A special processor design for Nucleotide Basic Local Alignment Search Tool with a new Banded two-hit method

Traditionally, sequence alignment is done by software. In this paper, we design a special processor based on Basic Local Alignment Search Tool for Nucleotides (BLASTn) with a new Banded Two-hit method. When compared to the results obtained from the ungapped BLASTn software, NCBI v2.2. 31+, our hardware always gives equal or better alignment results along with 2 to 6 times speed-up and a power consumption of only 370 mW.
Probabilistic Programming in Julia New Inference Algorithms

In this thesis we look at the design and development of a Probabilistic Programming Language (PPL) in Julia named Turing and the challenges of implementing the Hamiltonian Monte Carlo (HMC) sampler inside the Turing framework. This dissertation starts with a review of three important fields behind the project, which are Bayesian inference, general inference algorithms and probabilistic programming. This review provides theoretical foundations of the design of a universal PPL. Then some existing PPLs are reviewed, especially Stan and the up-to-date version of Turing. It is shown that, compared with Stan, Turing is more expressive and flexible in general. After that, the design and implementation of the HMC sampler is given. This part starts with the design of the compiler, in which a metaprogramming technique called macro is used to support three probabilistic syntax in Turing. Then the implementation of the standard HMC algorithm is discussed. In the Turing framework, two core ingredients of HMC, the target density function and the corresponding gradient function, are not straightforward to evaluate, which are the two main challenges of this project. The first issue is solved by building connections between the probabilistic program and the corresponding energy function required by HMC using Bayes’ rule, and the second one is accomplished by the use of Automatic Differentiation (AD) through probabilistic programs. Evaluations on the implemented HMC sampler have shown that the implementation is correct and the speed of the sampler is acceptable. Further improvements in terms of the performance of the HMC sampler and the functionality of Turing are proposed in the end. The main novel contributions of this thesis are a workable HMC sampler in Turing with acceptable performance as well as an updated version of the compiler which supports this HMC sampler and the further development of a Gibbs sampler combining HMC and PG.
Preparation and Characterization of Lignin Polyols from the Residues of Oil Palm Empty Fruit Bunch

In this work, lignin polyols were prepared from the liquefaction of kraft lignin and from the direct liquefaction of Elaeis guineensis lignocellulosic waste. The liquefaction reaction was performed with polyhydric alcohols using sulfuric acid as catalyst at 160 °C. The physical and chemical characterizations of lignin and lignin polyols were conducted by elemental analysis, Fourier transform-infrared spectroscopy, 1H and 13C nuclear magnetic resonance (NMR) spectroscopy, molecular weight distribution, and thermogravimetric analysis (TGA). Quantitative 13C NMR showed that all aliphatic hydroxyl group values of polyols noticeably increased with the use of the two methods compared to kraft lignin. The average molecular weight analysis of the liquefied product showed that it exhibited high molecular weight compared to kraft lignin. Both structural and thermal characteristics suggest that lignin polyols would be a good substitute for kraft lignin in the synthesis of polymeric compounds such as environmentally friendly resins or wood adhesives, as it presents higher amounts of activated free ring positions, higher molecular weight, and high thermal stability.
On the Equivalence and Impact on Stability of Impedance Modeling of Power Electronic Converters in Different Domains

Small-signal analysis of power electronic converters and systems is often carried out by impedance-based methods. At the core of these methods lies the impedance modeling, which can either be obtained through analytical calculations, simulations, or measurements. The impedance models can be obtained into two main domains: the dq-domain and the sequence domain. In the dq-domain, the impedance model is a $2\times 2$ matrix, while in the sequence domain, it is composed by the positive and negative sequence impedance. Recently, a third domain called the modified sequence domain was defined as an extension to the sequence domain, but also with clear similarities to the dq-domain. The objective of this paper is to unambiguously relate to each other the impedances in these three domains, and to show how this equivalence translates into their respective stability assessments. It is also proven that the sequence domain impedance has the same marginal stability condition as the dq-domain impedance matrix. The three-phase voltage source converter is used as an example converter in this paper, as its impedance model in all three domains is well established and reported by previous research. The results in this paper show that the modified sequence domain model can be derived from the dq-domain model (and vice versa), and that the stability analysis will be identical in these two domains. It is also shown how the original sequence domain model can be derived from the two other models through a model reduction. However, a small discrepancy between the two Nyquist plots is observed in the presence of components such as phase-locked loop or dc-link control.
Vitamin D: an ancient hormone

Abstract: Vitamin D has been produced by plants and animals almost from the time life began. The ability to transport and metabolize vitamin D to more active forms evolved as the structures of plants and animals became more complex, and the cells within these organisms took on more specialized functions. In higher‐order animals, the vitamin D receptor (VDR) is found in nearly every cell, and the ability of the cell to produce the active hormone, 1,25(OH)2D, is also widely distributed. Furthermore, the physiological functions with which vitamin D signalling is now associated are as diverse as the tissues in which the VDR is located. Why is this, and is there a common theme? This viewpoint article argues that there is. All cells maintain a fairly constant and submicromolar concentration of free calcium. Calcium is an important regulator of many processes within the cell. The ebb and flow of calcium within cells is controlled by calcium pumps, antiporters and channels. Animals with calcified exo‐ or endoskeletons have an additional need for calcium, a need that changes during the life cycle of the organism. In this article, I make the case that vitamin D signalling evolved to enable the organism to effectively regulate calcium flux, storage and signalling and that such regulation is critical for the evolutionary process.
A Bacterial Guanine Nucleotide Exchange Factor Activates ARF on Legionella Phagosomes

The intracellular pathogen Legionella pneumophilasubverts vesicle traffic in eukaryotic host cells to create a vacuole that supports replication. The dot/icm genes encode a protein secretion apparatus that L. pneumophila require for biogenesis of this vacuole. Here we show that L. pneumophilaproduce a protein called RalF that functions as an exchange factor for the ADP ribosylation factor (ARF) family of guanosine triphosphatases (GTPases). The RalF protein is required for the localization of ARF on phagosomes containing L. pneumophila. Translocation of RalF protein through the phagosomal membrane is adot/icm-dependent process. Thus, RalF is a substrate of the Dot/Icm secretion apparatus.
Kinetic Mechanism of GTP Binding and RNA Synthesis during Transcription Initiation by Bacteriophage T7 RNA Polymerase*

We have used stopped-flow and rapid chemical quench-flow methods to investigate the kinetics of the early steps during transcription initiation by bacteriophage T7 RNA polymerase. Most promoters of T7 RNA polymerase initiate with two GTPs. The kinetics of GTP binding was investigated by monitoring the fluorescence changes resulting from GTP binding to polymerase and fluorescent 2-aminopurine-containing promoter DNA complex. SchemeFS1 was determined from studies of T7 Φ10 promoter at 25 °C, where (E·D) n represents the polymerase·DNA complex in different conformations. GTPEand GTPI represent the elongating and initiating GTP molecules incorporated at the +2 and +1 positions, respectively. Our studies show that GTP at the elongation site binds with at least 10-fold tighter affinity than the GTP at the initiation site. Two conformational changes were revealed upon GTP binding to the polymerase·2-aminopurine DNA complex. The first conformational change occurred upon GTP binding to the elongation site. This conformational change was reversible, and studies with partially melted DNA and incorrect NTPs suggested that it may represent a DNA melting and/or base pairing step. A second rate-limiting conformational change whose rate was same as the maximum rate of pppGpG synthesis occurred after two GTPs were bound. As with DNA polymerases, this rate-limiting conformational change probably occurs at each NMP incorporation event and may be involved in proper positioning of the initiation and the elongating GTPs within the polymerase active site to achieve efficient and accurate RNA synthesis.
Set Constraints in Some Equational Theories

Set constraints are relations between sets of ground terms over a given alphabet. They give a natural formalism for many problems in program analysis, type inference, order-sorted unification, and constraint logic programming. In this paper we start studies of set constraints in the environment given by equational specifications. We show that in the case of associativity (i.e., in free monoids) as well as in the case of associativity and commutativity (i.e., in commutative monoids) the problem of consistency of systems of set constraints is undecidable; in linear nonerasing shallow theories the consistency of systems of positive set constraints is NEXPTIME-complete and in linear shallow theories the problem for positive and negative set constraints is decidable.
Supply Side Obstacles to Financing the Private Sector: Empirical Evidence from a Small Island Developing State

In light of the growing finance - private sector - economic growth findings, this article examines, from a supply - side perspective, obstacles to private sector financing in Fiji, a representative South Pacific small island, growth deprived, fragile economy. A survey of 80 percent of the formal financial sector suppliers reveals that financing the private sector may not be a major problem. However, the prevalent relationship - lending practices, good profits and well - managed risks also suggest that suppliers may be concentrating on a systematically selected small group of connected borrowers; the wider private sector, including many SMEs may be left out. Growth and development implications extend to developing economies beyond the South Pacific region.
Patient Mutations in Doublecortin Define a Repeated Tubulin-binding Domain*

Doublecortin (DCX) missense mutations are found in two clusters in patients with defective cortical neuronal migration. Although DCX can function as a microtubule-associated protein (MAP), the potential relationship between its MAP activity and neuronal migration is not understood. Here we show that the two clusters of patient mutations precisely define an internal tandem repeat. Each repeat alone binds tubulin, whereas neither repeat is sufficient for co-assembly with microtubules. The two tandem repeats are sufficient to mediate microtubule polymerization, and representative patient missense mutations lead to impaired polymerization both in vitro andin vivo as well as impaired microtubule stabilization. Furthermore, each repeat is predicted to have the secondary structure of a β-grasp superfold motif, a motif not found in other MAPs. The patient mutations are predicted to disrupt the structure of the motif, suggesting that the motif may be critical for the DCX-tubulin interaction. These data provide both genetic and biochemical evidence that the interaction of DCX with microtubules is dependent upon this novel repeated tubulin-binding motif.
Sex differences in angiotensin II‐stimulated fluid intake

What is the topic of this review? This report describes sex differences in the responses to angiotensin II, with a focus on fluid intake. What advances does it highlight? There are conflicting reports on the direction of the sex difference in fluid intake in response to angiotensin II. This review highlights how accounting for differences in body weight contributes to the discrepancies in the literature. In certain conditions, body weight influences fluid intake in a sex‐specific manner. This review also highlights the divergent effects of oestrogen receptor activation on fluid intake, which are likely to underlie the discussed sex differences.
Immunodeficiency-associated Vaccine-Derived Poliovirus Type 3 in Infant, South Africa, 2011

Patients with primary immunodeficiency are prone to persistently excrete Sabin-like virus after administration of live-attenuated oral polio vaccine and have an increased risk for vaccine-derived paralytic polio. We report a case of type 3 immunodeficiency-associated vaccine-derived poliovirus in a child in South Africa who was born with X-linked immunodeficiency syndrome.
Topology Regressive Distributed Model for Financial Time Series Prediction

Financial time series prediction has long been one of popular research areas for monetary policy makers, market participants and researchers. Inspired from the principle of self-organizing map, the author propose a topological regressive distributed model, which inherits the topology reserving advantage of self-organizing map and the simplicity of the normal autoregressive model. Comparison studies show the proposed method outperforms neural network based local model approaches and traditional autoregressive model on non-stationary financial time series (e.g. exchange rate, stock price).
Xenopus: An ideal system for chemical genetics

Chemical genetics, or chemical biology, has become an increasingly powerful method for studying biological processes. The main objective of chemical genetics is the identification and use of small molecules that act directly on proteins, allowing rapid and reversible control of activity. These compounds are extremely powerful tools for researchers, particularly in biological systems that are not amenable to genetic methods. In addition, identification of small molecule interactions is an important step in the drug discovery process. Increasingly, the African frog Xenopus is being used for chemical genetic approaches. Here, we highlight the advantages of Xenopus as a first‐line in vivo model for chemical screening as well as for testing reverse engineering approaches. genesis 50:207–218, 2012. © 2012 Wiley Periodicals, Inc.
Treatment of BCL-1 murine B-cell leukemia with recombinant cytokines. Comparative analysis of the anti-leukemic potential of interleukin 1 beta (IL-1 beta), interleukin 2 (IL-2), interleukin-6 (IL-6), tumor necrosis factor alpha (TNF alpha), granulocyte colony stimulating factor (G-CSF), granulocyte

Murine BCL-1 B-cell leukemia provides a model of disseminated human B-lineage acute lymphoblastic leukemia (ALL) and non-Hodgkins lymphoma (NHL). This model was used to evaluate and compare the anti-leukemic efficacy of recombinant cytokines rIL-1 beta, rIL-2, rIL-6, rTNF alpha, rG-CSF, rGM-CSF and their combinations. Of these 6 cytokines tested, rG-CSF, rIL-1 beta, rIL-2, and rTNF alpha exerted a marked anti-leukemia/lymphoma activity, as reflected by significantly improved survival of treated mice after inoculation of BCL-1 cells. Notably, no additive or synergistic effects were observed when 2-4 cytokines were used in combination. To our knowledge, this report represents the first comparative analysis of recombinant cytokine treatment regimens in an animal model of disseminated B-lineage ALL/NHL.
Clinical and functional significance of α9β1 integrin expression in breast cancer: a novel cell‐surface marker of the basal phenotype that promotes tumour cell invasion

Integrin α9β1 is a receptor for ECM proteins, including Tenascin‐C and the EDA domain of fibronectin, and has been shown to transduce TGFβ signalling. This study has examined the expression pattern of α9β1 in 141 frozen breast carcinoma samples and related expression to prognostic indices, molecular subtype and patient outcome. Effects of α9β1 on tumour cell migration and invasion were assessed using blocking antibody and gene transduction approaches. Integrin α9β1 localized to myoepithelial cells in normal ducts and acini, a pattern maintained in DCIS. A subset (17%) of invasive carcinomas exhibited tumour cell expression of α9β1, which related significantly to the basal‐like phenotype, as defined by either CK5/6 or CK14 expression. Tumour expression of α9β1 showed a significant association with reduced overall patient survival (p < 0.0001; HR 5.94, 95%CI 3.26–10.82) and with reduced distant‐metastasis‐free survival (p < 0.0001; HR 6.37, CI 3.51–11.58). A series of breast cancer cell lines was screened for α9β1 with the highly invasive basal‐like GI‐101 cell line expressing significant levels. Both migration and invasion of this line were reduced significantly in the presence of α9‐blocking antibody and following α9‐knockdown with siRNA. Conversely, migratory and invasive behaviour of α9‐negative MCF7 cells and α9‐low MDA MB468 cells was enhanced significantly by over‐expression of α9. Thus, α9β1 acts as a novel marker of the basal‐like breast cancer subtype and expression is associated with reduced survival, while its ability to promote breast cancer cell migration and invasion suggests that it contributes to the aggressive clinical behaviour of this tumour subtype. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Intensity and quality of warfarin anticoagulation in Chinese patients: setting the record straight.

See related article, p 23. North American and European guidelines for the use of warfarin for stroke prevention in patients with atrial fibrillation recommend routine coagulation monitoring and dose adjustment to achieve an international normalized ratio (INR) between 2 and 3.1,2 The quality of warfarin anticoagulation control is most commonly evaluated by calculating the time in therapeutic range (TTR) using the linear interpolation method of Rosendaal et al.3 Asian guidelines recommend a lower INR,4 based on the belief that Asian patients are more sensitive to the anticoagulant effects of warfarin and that they have unacceptably high rates of bleeding when the INR is maintained between 2 and 3. High-quality evidence to support targeting a lower INR range in Asian patients is lacking. In this issue, Ho et al5 report the results of a hospital-based registry of 8754 patients with nonvalvular atrial fibrillation and a CHA2DS2-VASc score >1 (mean enrolled between July 1997 and December 2011 who were followed up for a mean of 3 years). Patients with incomplete follow-up were not included. Clinical outcomes were obtained from the territory-wide information network of all public hospitals in Hong Kong. One thousand four hundred twenty-eight patients in the registry were …
Endovascular treatment of aneurysms associated with cerebral arteriovenous malformations: experiences after the introduction of Guglielmi detachable coils

The authors have treated 172 patients with arteriovenous malformation (AVM) since 1993. Among them, 25 patients had aneurysms with a total number of 43. The aneurysms were divided into four groups; proper feeder aneurysm (4), flow-related distal aneurysm (beyond the circle of Willis or M1, 7), flow-related proximal aneurysm (26) and remote aneurysm (6). Guglielmi detachable coil (GDC) embolisation was performed in 12 patients with 15 aneurysms. Gamma knife radiosurgery for AVM was performed in 10 of those 12 patients. Two of the proper feeder aneurysms were embolised with liquid material, together with the corresponding part of the AVM. The other aneurysms were treated surgically (14) or observed (12). There was no bleeding from aneurysms after treatment. In conclusion, GDC embolisation is a useful treatment for aneurysms associated with AVM, especially if the AVM is treated by radiosurgery. Liquid embolisation of a proper feeder aneurysm is one of the treatment options. Ltd.