Miracle-dz/UniFAR-FTUs huggingface dataset:
Processing: A Python Framework for the Seamless Integration of Geoprocessing Tools in QGIS

Processing is an object-oriented Python framework for the popular open source Geographic Information System QGIS, which provides a seamless integration of geoprocessing tools from a variety of different software libraries. In this paper, we present the development history, software architecture and features of the Processing framework, which make it a versatile tool for the development of geoprocessing algorithms and workflows, as well as an efficient integration platform for algorithms from different sources. Using real-world application examples, we furthermore illustrate how the Processing architecture enables typical geoprocessing use cases in research and development, such as automating and documenting workflows, combining algorithms from different software libraries, as well as developing and integrating custom algorithms. Finally, we discuss how Processing can facilitate reproducible research and provide an outlook towards future development goals.
SONOFUSION – FACT OR FICTION ?

Sonoluminescence and Sonofusion phenomena may occur when vapor bubbles implode. This paper reviews the status of our understanding of the bubble dynamics involved in these interesting phenomena. In particular, the experimental and analytical evidence supporting the observed production of neutrons and tritium due to thermonuclear fusion within imploding bubble clusters is reviewed. Moreover, potential methods to scale-up the neutron yield and some potential applications of this exciting new technology are discussed.
Inducible gene targeting in mice

A method of gene targeting that allows the inducible inactivation of a target gene in mice is presented. The method uses an interferon-responsive promoter to control the expression of Cre recombinase. Here, Cre was used to delete a segment of the DNA polymerase beta gene flanked by IoxP recombinase recognition sites. Deletion was complete in liver and nearly complete in lymphocytes within a few days, whereas partial deletion was obtained in other tissues. This method can be used for the inducible inactivation of any other gene in vivo.
Nanometer positioning of single quantum dots by flow control

We present a method to individually position single QDs with nanometer precision by electroosmotic flow control (EOFC). Using EOFC, we demonstrate the ability to individually select a QD from anywhere within a 100 µm control area inside a microfluidic chamber and place it at a desired position to with a 52 nm precision. The single photon emission of EOFC manipulated QDs is verified by photon anti-bunching. These results demonstrate, for the first time, the ability to position single QDs to nanometer position accuracy in a microflu-idic environment. Such capability opens up the possibility for controllable placement of QDs in nanophotonic structures for the development of complex quantum devices, as well as in situ study of QDs for biological and sensing applications.
Methodology of Building and Using Ontology for Providing Content-Based Access to Scientific Information Resources

The paper is devoted to the discussion on the problem of provision of the content-based access to scientific information resources. We suggest solving this problem by means of creation of specialized topic-oriented Internet portals. The information basis of such portals is an ontology that supports integration of information resources relevant to the subject domain of a portal into a uniform information space and provides formulation of user queries in terms of the subject domain and knowledge-driven navigation through the information space of the portal.
MicroRNA-224 Negatively Regulates p21 Expression During Late Neoplastic Progression in Inflammatory Bowel Disease

Background:The development of colon cancer represents a major complication in patients with inflammatory bowel disease (IBD). The importance of microRNAs (miRs) in carcinogenesis is becoming clearer because miRs have been implicated in the regulation of cancer-related cellular processes to include apoptosis, differentiation, cell cycle progression, and immune function. In the current study, we sought to identify miR dysregulation specific to progression along the normal-inflammation-cancer axis in colonic specimens from patients with IBD. Methods:MiR microarrays and quantitative reverse transcription PCR were used to detect and confirm dysregulated miRs. Receiver operating characteristic curve analysis was applied to evaluate the potential use of miR-224 as a neoplastic disease marker in IBD. For miR-224 target messenger RNA (mRNA) identification, mRNA microarrays were employed in combination with bioinformatic analyses, Western blotting, and luciferase activity measurements. Results:We identified 30 miRs that were differentially expressed between chronically inflamed mucosae and cancers arising from IBD tissues. MiR-224 levels increased successively at each stage of IBD progression and accurately discriminated cancers from normal or chronically inflamed IBD tissues. Moreover, mRNA arrays combined with bioinformatic analyses suggested the participation of miR-224 in cell cycle regulation. Subsequently, cell cycle experiments indicated that miR-224 regulates the G1-S checkpoint. Finally, in silico prediction analyses, confirmed by Western blotting and luciferase assays, identified p21 as a specific direct mRNA target of miR-224. Conclusions:These findings reveal miR dysregulation specific to IBD-associated colorectal carcinoma. MiR-224 is overexpressed in IBD cancers and targets p21, a key cell cycle regulator. Moreover, these results establish the participation of miR-224 in IBD carcinogenesis.
Tracking Manipulator Trajectories With Ordinary Singularities: A Null Space-Based Approach

This article discusses the problem of tracking manipulator end-link trajectories passing through ordinary singularities. It is based on a method developed recently by Kieffer (1992), who suggested parameterizing the end-link trajectory with a parameter that is not time, and considering this parameter as a dependent variable. We show that this is equivalent to a kinematically redundant mechanism comprising the original nonredundant kinematic chain augmented by one more virtual link. The trajectory is actually mapped onto the joint space augmented by the parameter variable. Although the new mech anism performs only a "self-motion" tracking of the projected trajectory through regular points and ordinary singularities, the end-link of the real mechanism tracks the desired trajec tory. Our solution is based on effective null space methods that have been widely applied to kinematically redundant manipula tors. Asymptotic convergence of the tracking error to zero and stability is guaranteed through a closed-loop approach.
SPECT–Negative SIRPIDs Argues Against Treatment as Seizures

Summary Stimulus-induced rhythmic, periodic, or ictal discharges (SIRPIDs) are a recently described form of epileptiform periodic discharges evoked by arousal. Similar to other periodic discharges (e.g., pseudoperiodic lateralized epileptiform discharges, generalized periodic epileptiform discharges, bilaterally independent epileptiform discharges), SIRPIDs lie somewhere along an ictal–interictal continuum. To determine whether SIRPIDs represent an ictal phenomenon reflected by increased focal cerebral perfusion on single-photon emission computerized tomography, or conversely an interictal pattern, the authors tested a patient with nonconvulsive status confirmed on EEG, which evolved to SIRPIDs with a concomittant contralateral hemiparesis. To test the ictal-increased flow hypothesis, a single-photon emission computerized tomography scan was obtained during a stimulus-induced train of rhythmic discharges on EEG, but it revealed no increase in tracer uptake. The authors conclude that SIRPIDs did not increase regional cerebral blood flow as would seizures. Thus, the evidence indicates little if any metabolic/blood flow activation with SIRPIDs, thus tempering the intensity with which SIRPIDs might be managed. This provides a testable paradigm for future patterns of uncertain epileptic significance.
Hodgkin lymphoma: MOPP chemotherapy to PD‐1 blockade and beyond

Hodgkin lymphoma is a rare lymphoid malignancy affecting ∼9,200 new patients in the United States annually. Progress in the management of this disease over the past 50 years has been remarkable and the prognosis of this malignancy has changed from a uniformly fatal process to one in which the vast majority of patients are expected to be cured. This remarkable progress has been due to the use of combination approaches incorporating chemotherapy and radiation therapy, and now more recently antibody‐drug conjugates and immune checkpoint inhibitors. The goal for the future is to develop treatment combinations that successfully treat all patients and markedly decrease the long‐term side effects. Am. J. Hematol. 91:109–112, 2016. © 2015 Wiley Periodicals, Inc.
Replication fork block protein, Fob1, acts as an rDNA region specific recombinator in S. cerevisiae

Background: The analysis of homologous recombination in the tandemly repeating rDNA array of Saccharomyces cerevisiae should provide useful information about the stability of not only the rDNA repeat but also the abundant repeated sequences on higher eukaryotic genomes. However, the data obtained so far are not yet conclusive, due to the absence of a reliable assay for detecting products of recombination in the rDNA array.
The secretion of the denervated adrenal medulla of the cat.

In 1917 Stewart and Rogoff tried to determine whether the chronically denervated adrenal medulla shows any secretory activity. They came to the conclusion that " no epinephrine is normally released except through nerves. " In view of the recent development of sensitive methods for the detection of adrenaline and noradrenaline, and in view of the possible role played by noradrenaline in the maintenance of vascular tone, the problem was reinvestigated.
Deletion mapping of a mouse hepatitis virus defective interfering RNA reveals the requirement of an internal and discontiguous sequence for replication

All of the defective interfering (DI) RNAs of mouse hepatitis virus (MHV) contain both the 5' and 3' ends of the viral genomic RNA, which presumably include the cis sequences required for RNA replication. To define the replication signal of MHV RNA, we have used a vaccinia virus-T7 polymerase-transcribed MHV DI RNA to study the effects of sequence deletion on DI RNA replication. Following infection of susceptible cells with a recombinant vaccinia virus expressing T7 RNA polymerase, various cDNA clones derived from a DI RNA (DIssF) of the JHM strain of MHV, which is a 3.5-kb naturally occurring DI RNA, behind a T7 promoter were transfected. On superinfection with a helper MHV, the ability of various DI RNAs to replicate was determined. Serial deletions from the middle of the RNA toward both the 5' and 3' ends demonstrated that 859 nucleotides from the 5' end and 436 nucleotides from the 3' end of the MHV RNA genome were necessary for RNA replication. Surprisingly, an additional stretch of 135 nucleotides located at 3.1 to 3.3 kb from the 5' end of the genome was also required. This stretch is discontiguous from the 5'-end cis replication signal and is present in all of the naturally occurring DI RNAs studied so far. The requirement for a long stretch of 5'- and 3'-end sequences predicts that the subgenomic MHV mRNAs cannot replicate. The efficiency of RNA replication varied with different cDNA constructs, suggesting possible interaction between different regions of DI RNA. The identification of MHV RNA replication signals allowed the construction of an MHV DI-based expression vector, which can express foreign genes, such as the chloramphenicol acetyltransferase gene.
Preoperative chemotherapy in primary operable breast cancer: results from the European Organization for Research and Treatment of Cancer trial 10902.

PURPOSE To evaluate whether preoperative neoadjuvant chemotherapy in patients with primary operable breast cancer results in better overall survival (OS) and relapse-free survival rates and whether preoperative chemotherapy permits more breast-conserving surgery procedures than postoperative chemotherapy. PATIENTS AND METHODS Six hundred ninety-eight breast cancer patients (T1c, T2, T3, T4b, N0 to 1, and M0) were enrolled onto a randomized phase III trial that compared four cycles of fluorouracil, epirubicin, and cyclophosphamide administered preoperatively versus the same regimen administered postoperatively (the first cycle administered within 36 hours after surgery). Patients were followed up for OS, progression-free survival (PFS), and locoregional recurrence (LRR). RESULTS At a median follow-up of 56 months, there was no significant difference in terms of OS (hazards ratio, 1.16; P =.38), PFS (hazards ratio, 1.15; P =.27), and time to LRR (hazards ratio, 1.13; P =.61). Fifty-seven patients (23%) were downstaged by the preoperative chemotherapy, whereas 14 patients (18%) underwent mastectomy and not the planned breast-conserving therapy. CONCLUSION The use of preoperative chemotherapy yields similar results in terms of PFS, OS, and locoregional control compared with conventional postoperative chemotherapy. In addition, preoperative chemotherapy enables more patients to be treated with breast-conserving surgery. Because preoperative chemotherapy does not improve disease outcome compared with postoperative chemotherapy, future trials should involve quality-of-life studies to investigate whether patients will benefit from this treatment modality.
Effects of Environmental Factors on Polychaete Assemblage in Penang National Park, Malaysia

Macrobenthos distribution along the coastal waters of Penang National Park was studid to estimate the effect of different environmental parameters at three stations, during six sampling months, from June 2010 to April 2011. The aim of this survey was to investigate different environment stress over soft bottom polychaete community along Teluk Ketapang and Pantai Acheh (Penang National Park) over a year period. Variations in the polychaete community were evaluated using univariate and multivariate methods. A total of 604 individuals were examined which was grouped into 23 families. Family Nereidae was the most abundant (22.68%), followed by Spionidae (22.02%), Hesionidae (12.58%), Nephtylidae (9.27%) and Orbiniidae (8.61%). It is noticeable that good results can only be obtained on the basis of good taxonomic resolution. The maximum Shannon-Wiener diversity (H′=2.16) was recorded at distance 200m and 1200m (August 2010) in Teluk Ketapang and lowest value of diversity was found at distance 1200m (December 2010) in Teluk Ketapang. Keywords—Polychaete assemblage, environment factor, Pantai Acheh, Teluk Ketapang.
Fuzzy Cluster Head Election algorithm based on LEACH protocol for wireless sensor networks

Low-Energy Adaptive Clustering Hierarchy (LEACH) is the most famous hierarchical routing algorithms that optimizes energy consumption and increases the lifetime of network. However, the main drawback of this protocol is the randomly selection of Cluster Head (CH) without caring about remaining energy of the node, the number of neighbors alive within cluster range or the distance between node and the sink. In this work, we propose a fuzzy CH election algorithm based on LEACH protocol. In fact, this algorithm uses Fuzzy Logic method and takes into account the three criteria mentioned above. Our simulation results are compared with LEACH, Cluster Head Election using Fuzzy logic (CHEF) and Fuzzy Energy-Aware Unequal Clustering algorithm (EAUCF) and demonstrate that our proposed approach outperforms these algorithms in term of prolonging the lifetime of network and saving residual energy.
Maternal Height as a Risk Factor for Caesarean Section Due to Failure to Progress in Labour

Summary: We examined for a regional sample of the New Zealand population, the relationship between maternal height and an increased risk of emergency Caesarean section due to arrested labour, to identify a height below which the risk of Caesarean section increases markedly and to quantify the risk of a Caesarean section for a range of maternal heights. The data of nulliparous singleton pregnancies over the period 1994–1998 was sorted into 2 study groups, one resulting in emergency Caesarean section for arrested labour and the other a group of women who had normal vaginal delivery requiring no intervention. The means and standard deviations of these 2 groups were found and 99% confidence intervals calculated. They were analysed for statistical difference and then a logistical regression calculation tried to identify a height at which the risk of a Caesarean section increased suddenly. There were 81 women in the Caesarean section group and 997 in the normal vaginal delivery group. Mean heights and confidence intervals were 161.0 cm (158.9–163.1) and 164.6 cm (164.0–165.2) respectively. There was a statistically significant difference between these means (p < 0.001) but logistic regression analysis showed that risk of Caesarean section increased gradually with decreasing height, and even then did not reach more than 30% risk until a height of less than 140 cm. Low maternal height was associated with increased risk of Caesarean section due to labour arrest. Because the likelihood of having a normal vaginal delivery was still very good (> 80%) at modest degrees of short stature, this risk factor alone is unlikely to affect management. However the combination of other risk factors with maternal height may be of clinical use.
Automatic superresolution image reconstruction based on hybrid MAP-POCS

Image superresolution (SR) reconstruction refers to methods that increase image spatial resolution by fusing information from either a sequence of temporal adjacent images or multi-source images from different sensors. In the paper we propose a hybrid MAP-POCS method for automatic image SR reconstruction, which firstly estimates the unknown point spread function (PSF) and an approximation for the original ideal image, and then sets up the HMRF image prior model and assesses its inhomogeneous control parameter through maximum likelihood (ML) estimation, finally automatically computes the regularized solution by two-phase iterative solution. Hybrid MAP-POCS estimates computed on simulation images, actual video sequence and actual satellite images show dramatic visual and quantitative improvements over bilinear interpolation and ML-POCS reconstruction results with sharp edges, correctly restored textures and a high PSNR improvement.
On projections of selfadjoint operators and operator product adjoints

The purpose of this department is to provide early announcement of significant new results, with some indications of proof. Although ordinarily a research announcement should be a brief summary of a paper to be published in full elsewhere, papers giving complete proofs of results of exceptional interest are also solicited. Manuscripts more than eight typewritten double spaced pages long will not be considered as acceptable.
Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

Fong et al. examined cotranscriptional pre-mRNA splicing using RNA polymerase II mutants that change average elongation rates genome-wide. Slow and fast elongation affected constitutive and alternative splicing and often both increased or both decreased inclusion of a particular exon or retained intron. These results suggest that an optimal rate of transcriptional elongation is required for normal cotranscriptional pre-mRNA splicing.
Metal-insulator transition in AlxGa1-xAs/GaAs heterostructures with large spacer width.

Analytical results are presented for the mobility of a two-dimensional electron gas in a heterostructure with a thick spacer layer \ensuremath{\alpha}. Due to multiple-scattering effects a metal-insulator transition occurs at a critical electron density ${\mathit{N}}_{\mathit{c}}$=${\mathit{N}}_{\mathit{i}}^{1/2}$/(4${\mathrm{\ensuremath{\pi}}}^{1/2}$\ensuremath{\alpha}) (${\mathit{N}}_{\mathit{i}}$ is the impurity density). The transport mean free path ${\mathit{l}}^{(\mathit{t})}$ (calculated in Born approximation) at the metal-insulator transition is ${\mathit{l}}_{\mathit{c}}^{(\mathit{t})}$=2\ensuremath{\alpha}. A localization criterion in terms of the renormalized single-particle mean free path ${\mathit{l}}^{(\mathrm{sr})}$ is presented: ${\mathit{k}}_{\mathit{F}\mathit{c}}$${\mathit{l}}_{\mathit{c}}^{(\mathrm{sr})}$=(1/2${)}^{1/2}$ (${\mathit{k}}_{\mathit{F}\mathit{c}}$ is the Fermi wave number at the critical density). I compare the theoretical results with recent experimental results found in ${\mathrm{Al}}_{\mathit{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$As/GaAs heterostructures with large spacer width: 12002800 \AA{}. Remote impurity doping and homogeneous background doping are considered. The only fitting parameter used for the theoretical results is the background doping density ${\mathit{N}}_{\mathit{B}}$=6\ifmmode\times\else\texttimes\fi{}${10}^{13}$ ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}3}$. My theory is in fair agreement with the experimental results.
Co-transplantation of hippocampal neural stem cells and astrocytes and microvascular endothelial cells improve the memory in ischemic stroke rat.

BACKGROUND Neural stem cells (NSCs) are promising for ischemia stroke because they can replace damaged or lost cells. However, the adult central nervous system (CNS) does not provide an optimal microenvironment for exogenous NSCs to survive, proliferation and differentiation. We established a co-transplantation system with NSCs and astrocyte and brain microvascular endothelial cells (BMECs) to explore whether it can improve the memory ability in ischemic stroke rat. METHODS After building the ischemic stroke in 50 rats by middle cerebral artery occlusion and reperfusion (MCAO/R), transplantation of NSCs and astrocyte and BMECs were performed with different combination. RESULTS Laser doppler flowmetry and MRI were used to detect the ischemia of the model and 42 rats survived for the Morris water-maze test. The test shows that co-transplantation with the three different cells together can improve memory deficits in MCAO/R rat and it is the most effect group. Grafting with two cells have more effect in memory improving than one cell while transplanting NSC alone has no obvious effect on memory improving. CONCLUSIONS In NSC niche, astrocytes and BMECs are the most important cells to regulate and interaction with NSCs. Co-transplantation NSCs with astrocyte and BMECs can improve the memory ability in ischemia rat, which maybe the result of microenvironment improve by the astrocyte and BMECs.
Error analysis in finite difference solution of linear and non-linear cylindrical magnetostatic problems

This paper poses a magnitostatic problem in cylindrical coordinate with different permeabilities for each region. In this problem the boundary condition of the third kind is utilized. This problem is solved using the finite element and finite difference methods and also the analytical solutions for the linear case. The finite difference results of the finite difference method show low magnetic vector potential as well as the magnetic flux density when compared to the finite element results and in the linear case, to the analytical solution. This paper investigates the cause and the dependency of error production to the number of mesh points (grid size) selected and the permeability of the medium when using the finite difference method in conjunction with boundary condition of the third kind. It then, presents a complete error analysis for different material permeability and grid size selections used for the core in the linear and non-linear cases. It also shows a technique to overcome the problem of low magnetic flux density calculation using the finite difference method. The results obtained by the new technique shows close agreement with the finite element method as well as the analytical solution.