Miracle-dz/UniFAR-FTUs huggingface dataset:
GIS-based examination of peats and soils in Surfers Paradise, Australia

Abstract The subsoil conditions of Surfers Paradise in Southeast Queensland of Australia have been examined in terms of soil stiffness by using geographic information system (GIS). Peat is a highly organic and compressible material. Surfers Paradise (as a study area) has problematic peat layer due to its high water content, high compressibility, and low shear strength. This layer has various thicknesses at different locations ranging between R.L. 10 to R.L. -19.6 m. Buildings in Surfers Paradise are using piled foundations to avoid the high compressibility and low shear strength peat layer. Spatial Analyst extension in the GIS ArcMap10 has been utilised to develop zonation maps for different depths in the study area. Each depth has been interpolated as a surface to create Standard Penetration Test SPT-N value GIS-based zonation maps for each depth. In addition, 8 interpolation techniques have been examined to evaluate which technique gives better representation for the Standard Penetration Test (SPT) data. Inverse Distance weighing (IDW) method in Spatial Analyst extension gives better representation for the utilised data with certain parameters. Two different cross sections have been performed in the core of the study area to determine the extent and the depth of the peat layer underneath already erected buildings. Physical and engineering properties of the Surfers Paradise peat have been obtained and showed that this peat falls within the category of tropical peat.
Prognostic Value of Combination of Pretreatment Red Cell Distribution Width and Neutrophil-to-Lymphocyte Ratio in Patients with Gastric Cancer

Aims Gastric cancer (GC) is often diagnosed at an advanced stage; inexpensive and valid biomarkers for GC are still unavailable. We aimed to evaluate the prognosis of the combination of pretreatment red cell distribution width (RDW) and neutrophil-to-lymphocyte ratio (NLR) in patients with GC. Methods A retrospective analysis from 103 GC patients who were diagnosed at our institution from 2012 to 2016 was performed. Both pretreatment RDW and NLR were calculated based on the recommended cutoff values of 13.4% and 2.755, respectively. Combined values of RDW and NLR (RDW + NLR) stratified patients into a score of 0 (RDW ≤ 13.4% and NLR ≤ 2.755), a score of 1 (RDW > 13.4% or NLR > 2.755), and a score of 2 (RDW > 13.4% and NLR > 2.755). Prognostic significances for overall survival (OS) and progression-free survival (PFS) were assessed. Results Pretreatment RDW + NLR was a significantly independent prognostic factor for OS and PFS. Moreover, high RDW + NLR was strongly related to age, tumor location, TNM stage, CA125, and CA199. In a subgroup analysis for patients with advanced gastric cancer (AGC), we observed that the level of RDW + NLR was markedly associated with OS and PFS. Conclusion Pretreatment RDW + NLR is a simple, inexpensive, and valid prognostic system to predict the survival in patients with GC, especially AGC.
GP3: GenePix post-processing program for automated analysis of raw microarray data

UNLABELLED Here we describe an automated and customizable program to correct, filter and normalize raw microarray data captured using GenePix, a commonly used microarray image analysis application. Files can be processed individually or in batch mode for increased throughput. User defined inputs specify the stringency of data filtering and the method and conditions of normalization. The output includes gene summaries for replicate spots and descriptive statistics for each experiment. The source code (Perl) can also be adapted to handle raw data output from other image analysis applications. AVAILABILITY http://bch.msu. edu/~zacharet/microarray/GP3.html
The Influence of End‐of‐Life Care on Organ Donor Potential

Many patients with acute devastating brain injury die outside intensive care units and could go unrecognized as potential organ donors. We conducted a prospective observational study in seven hospitals in the Netherlands to define the number of unrecognized potential organ donors outside intensive care units, and to identify the effect that end‐of‐life care has on organ donor potential. Records of all patients who died between January 2013 and March 2014 were reviewed. Patients were included if they died within 72 h after hospital admission outside the intensive care unit due to devastating brain injury, and fulfilled the criteria for organ donation. Physicians of included patients were interviewed using a standardized questionnaire regarding logistics and medical decisions related to end‐of‐life care. Of the 5170 patients screened, we found 72 additional potential organ donors outside intensive care units. Initiation of end‐of‐life care in acute settings and lack of knowledge and experience in organ donation practices outside intensive care units can result in under‐recognition of potential donors equivalent to 11–34% of the total pool of organ donors. Collaboration with the intensive care unit and adjusting the end‐of‐life path in these patients is required to increase the likelihood of organ donation.
The Human Replicative Helicase, the CMG Complex, as a Target for Anti-cancer Therapy

DNA helicases unwind or rearrange duplex DNA during replication, recombination and repair. Helicases of many pathogenic organisms such as viruses, bacteria, and protozoa have been studied as potential therapeutic targets to treat infectious diseases, and human DNA helicases as potential targets for anti-cancer therapy. DNA replication machineries perform essential tasks duplicating genome in every cell cycle, and one of the important functions of these machineries are played by DNA helicases. Replicative helicases are usually multi-subunit protein complexes, and the minimal complex active as eukaryotic replicative helicase is composed of 11 subunits, requiring a functional assembly of two subcomplexes and one protein. The hetero-hexameric MCM2-7 helicase is activated by forming a complex with Cdc45 and the hetero-tetrameric GINS complex; the Cdc45-Mcm2-7-GINS (CMG) complex. The CMG complex can be a potential target for a treatment of cancer and the feasibility of this replicative helicase as a therapeutic target has been tested recently. Several different strategies have been implemented and are under active investigations to interfere with helicase activity of the CMG complex. This review focuses on the molecular function of the CMG helicase during DNA replication and its relevance to cancers based on data published in the literature. In addition, current efforts made to identify small molecules inhibiting the CMG helicase to develop anti-cancer therapeutic strategies were summarized, with new perspectives to advance the discovery of the CMG-targeting drugs.
A Kernel Theory of Modern Data Augmentation

Data augmentation, a technique in which a training set is expanded with class-preserving transformations, is ubiquitous in modern machine learning pipelines. In this paper, we seek to establish a theoretical framework for understanding data augmentation. We approach this from two directions: First, we provide a general model of augmentation as a Markov process, and show that kernels appear naturally with respect to this model, even when we do not employ kernel classification. Next, we analyze more directly the effect of augmentation on kernel classifiers, showing that data augmentation can be approximated by first-order feature averaging and second-order variance regularization components. These frameworks both serve to illustrate the ways in which data augmentation affects the downstream learning model, and the resulting analyses provide novel connections between prior work in invariant kernels, tangent propagation, and robust optimization. Finally, we provide several proof-of-concept applications showing that our theory can be useful for accelerating machine learning workflows, such as reducing the amount of computation needed to train using augmented data, and predicting the utility of a transformation prior to training.
Formal Description and Verification of a Text-based Model Differencing and Merging Method

Version control is an integral part of teamwork in software development. Differencing and merging key artifacts (i.e. source code) is a key feature in version control systems. The concept of version control can also be applied to model-driven methodologies. The models are usually differenced and merged in their graph-based form. However, if supported, we can also use the textual representation of the models during this process. Text-based model differencing and merging methods have some useful use cases, like supporting the persistence of the model, or having a fallback plan should the differencing algorithm fail. Using the textual notation to display and edit models is relatively rare, as the visual (graph-based) representation of the model is more common. However, many believe that using them both would be the ideal solution. In this paper, we present the formal description of a text-based model differencing and merging method from previous work. We also verify our algorithm based on this formal description. The focus of the verification is the soundness and completeness of the method. The long term goal of our research is to develop a modeling environment-independent algorithm. This could be used in version control systems that support textual representations.
Efficient Spectrum Availability Information Recovery for Wideband DSA Networks: A Weighted Compressive Sampling Approach

There have recently been research efforts that leverage compressive sampling to enable wideband spectrum sensing recovery at sub-Nyquist rates. These efforts consider homogenous wideband spectrum, where all bands are assumed to have similar primary user traffic characteristics. In practice, however, wideband spectrum is not homogeneous, in that different bands could present different occupancy patterns. In fact, applications of similar types are often assigned spectrum bands within the same block, dictating that wideband spectrum is indeed heterogeneous. In this paper, we consider heterogeneous wideband spectrum and exploit its inherent block-like structure to design efficient compressive spectrum sensing techniques that are well suited for heterogeneous wideband spectrum. We propose a weighted $\ell _{1}$ -minimization sensing information recovery algorithm that achieves more stable recovery than that achieved by existing approaches, while accounting for the variations of spectrum occupancy across both the time and frequency dimensions. In addition, we show that our proposed algorithm requires a smaller number of sensing measurements when compared to the state-of-the-art approaches.
Agglomeration, (un)‐related variety and new firm survival in China

We study empirically the effects of five different dimensions of agglomeration – specialization, diversity, related variety, unrelated variety, and city size – on the survival chances of new entrepreneurial firms in China. Consideration is further given to studying the mediating effects of local subsidies on new firm survival given different existing local industrial structures in those regions. In support of the ‘regional branching’ hypothesis, we find that increasing local related variety has a stronger positive effect on new firm survival than other types of agglomeration. We also find that receiving comparatively fewer subsidies motivates firms to seek out and benefit from local existing economies, which in turn, positively influence their chances of survival. By contrast, agglomerated firms that receive relatively more subsidies tend to be more likely to face financial distress leading to eventual market exit. The findings thus reveal that both the intensity and the location of state support matters in terms of optimizing positive agglomeration effects on firms' post‐entry performance and survival. Se estudia empiricamente los efectos de cinco dimensiones diferentes de la aglomeracion (especializacion, diversidad, variedad relacionada, variedad no relacionada y tamano de la ciudad) sobre las posibilidades de supervivencia de las nuevas empresas emprendedoras en China. Ademas, se considera el estudio los efectos mediadores de las subvenciones locales en la supervivencia de las nuevas empresas, habida cuenta de las diferentes estructuras industriales locales existentes en esas regiones. En apoyo de la hipotesis de ‘ramificacion regional’, se encontro que el aumento de la variedad relacionada local tiene un efecto positivo mas fuerte sobre la supervivencia de las nuevas empresas que otros tipos de aglomeracion. Tambien se encontro que recibir comparativamente menos subsidios motiva a las empresas a buscar y beneficiarse de las economias locales existentes, lo que a su vez influye positivamente en sus posibilidades de supervivencia. Por el contrario, las empresas de una aglomeracion que reciben relativamente mas subvenciones tienden a tener mas probabilidades de enfrentarse a dificultades financieras que las lleven a una eventual retirada del mercado. Asi pues, los resultados revelan que tanto la intensidad como la ubicacion del apoyo estatal son importantes para optimizar los efectos positivos de la aglomeracion en el rendimiento y la supervivencia de las empresas despues de su entrada en el mercado. 本稿では、集積の5つの側面、すなわち、特殊化、多角化、関係的多様性、非関係的多様性、首都の規模、以上が中国の新規ベンチャー企業が存続する確率に及ぼす効果を実証的に検証する。 その地域における既存の産業の構造にいくつかの種類がある場合の、地方交付金が新規企業の存続に対する効果を媒介することの研究も考慮に入れる。 ‘regional branching’仮説を支持するように、地方の関係的多様性の増加は、新規企業の存続に対して、他のタイプの集積よりもより強い正の効果を与えていることが認められる。 また、受給される交付金が比較的少ないことは、企業が、模索して地域の既存の経済から恩恵を受けるための動機づけとなり、その結果として企業の存続の可能性にプラスの影響をもたらしていることがわかる。 一方、比較的多く交付金を受給している集積内の企業は、財政難に陥りやすく結果的に廃業となりやすい傾向がある。 以上のように、知見から、国家支援の強さと立地の両方が、企業の参入後の業績と存続に対する正の集積効果の最適化において非常に重要であることが示された。
Numerical investigation of a plunging airfoil

The goal of this thesis is to investigate vortex dynamics of a plunging airfoil by studying the vorticity transport mechanisms of two-dimensional simulations. Direct numerical simulations were implemented in an e↵ort to provide detailed flow fields that are di cult to capture with experimental methods. The simulations were used to study a simplified flat airfoil in a freestream that was subject to pure plunging motion. Due to computational limits, it was not practical to simulate in three-dimensions and the results are limited to two-dimensions. Quantitative and qualitative analyses were used the validate the two-dimensional simulations and gain insight into the e↵ects of eliminating three-dimensional physics in a nominally two-dimensional flow. Additionally, a parametric study was conducted to analyze the e↵ects of Reynolds and Strouhal numbers on the transport of vorticity.
Azole-Resistance in Aspergillus terreus and Related Species: An Emerging Problem or a Rare Phenomenon?

Objectives: Invasive mold infections associated with Aspergillus species are a significant cause of mortality in immunocompromised patients. The most frequently occurring aetiological pathogens are members of the Aspergillus section Fumigati followed by members of the section Terrei. The frequency of Aspergillus terreus and related (cryptic) species in clinical specimens, as well as the percentage of azole-resistant strains remains to be studied. Methods: A global set (n = 498) of A. terreus and phenotypically related isolates was molecularly identified (beta-tubulin), tested for antifungal susceptibility against posaconazole, voriconazole, and itraconazole, and resistant phenotypes were correlated with point mutations in the cyp51A gene. Results: The majority of isolates was identified as A. terreus (86.8%), followed by A. citrinoterreus (8.4%), A. hortai (2.6%), A. alabamensis (1.6%), A. neoafricanus (0.2%), and A. floccosus (0.2%). One isolate failed to match a known Aspergillus sp. , but was found most closely related to A. alabamensis. According to EUCAST clinical breakpoints azole resistance was detected in 5.4% of all tested isolates, 6.2% of A. terreus sensu stricto (s.s.) were posaconazole-resistant. Posaconazole resistance differed geographically and ranged from 0% in the Czech Republic, Greece, and Turkey to 13.7% in Germany. In contrast, azole resistance among cryptic species was rare 2 out of 66 isolates and was observed only in one A. citrinoterreus and one A. alabamensis isolate. The most affected amino acid position of the Cyp51A gene correlating with the posaconazole resistant phenotype was M217, which was found in the variation M217T and M217V. Conclusions: Aspergillus terreus was most prevalent, followed by A. citrinoterreus. Posaconazole was the most potent drug against A. terreus, but 5.4% of A. terreus sensu stricto showed resistance against this azole. In Austria, Germany, and the United Kingdom posaconazole-resistance in all A. terreus isolates was higher than 10%, resistance against voriconazole was rare and absent for itraconazole.
Closing the sensorimotor loop: haptic feedback facilitates decoding of motor imagery

The combination of brain–computer interfaces (BCIs) with robot-assisted physical therapy constitutes a promising approach to neurorehabilitation of patients with severe hemiparetic syndromes caused by cerebrovascular brain damage (e.g. stroke) and other neurological conditions. In such a scenario, a key aspect is how to reestablish the disrupted sensorimotor feedback loop. However, to date it is an open question how artificially closing the sensorimotor feedback loop influences the decoding performance of a BCI. In this paper, we answer this issue by studying six healthy subjects and two stroke patients. We present empirical evidence that haptic feedback, provided by a seven degrees of freedom robotic arm, facilitates online decoding of arm movement intention. The results support the feasibility of future rehabilitative treatments based on the combination of robot-assisted physical therapy with BCIs.
Language Matters

Context: In order to gain competitive advantages in the global market, many software outsourcing organizations in non- English speaking countries adopted the use of English as the lingua franca mandate in their organizations. Goal: We sought to assess the influence of the English lingua franca mandate on the teamwork in software outsourcing vendors empirically. Approach: We conducted a field experiment performed in a Chinese software outsourcing company. We measured the team-work related constructs repeatedly with the progress of field experiment process. Results: This study reveals enforcing the English lingua franca may lead to: (1) lower satisfaction at work, (2) the decrease of teamwork quality, and (3) the lack of coordination in terms of social-technical congruence. Conclusion: Decision makers may need to be careful before launching the English lingua franca mandate. We also conceptually discusses how the English lingua franca mandate's influence on software quality. In a broader sense, the research calls attentions to the ``language'' issues in global software engineering practices, which is well-known but has not yet received enough attentions in software engineering research.
The effects of celery leaf (apium graveolens L.) treatment on blood glucose and insulin levels in elderly pre-diabetics

Objectives: To analyze the effect of celery leaf extract on blood glucose and plasma insulin levels in elderly pre-diabetics. Methods: This study was conducted between March and November 2014 at the Faculty of Medicine, Syiah Kuala University, Banda Aceh, Indonesia. A quasi-experimental pretest-posttest with a control group was conducted with elderly pre-diabetic volunteers. The subjects included 16 elderly pre-diabetics older than 60 (6 males and 10 females). The subjects were randomly divided into 2 groups: a control group (placebo-treated) and a treatment group (celery-treated). The treatment consisted of celery leaf extract capsules at the dose of 250 mg, 3 times per day (morning, afternoon and evening), 30 minutes before a meal, for 12 days. Data analysis was performed using the t-test (p<0.05). Results: There was a significant decrease in pre-prandial plasma glucose levels (p=0.01) and post-prandial plasma glucose levels (p=0.00), but no significant increase in plasma insulin levels (p=0.15) after celery leaf treatment in elderly pre-diabetics. Conclusion: Celery was effective at reducing blood glucose levels, but there was a lack of association between blood glucose levels and plasma insulin levels in elderly pre-diabetics.
Development of Tract‐Specific White Matter Pathways During Early Reading Development in At‐Risk Children and Typical Controls

Abstract Developmental dyslexia is a neurodevelopmental disorder with a strong genetic basis. Previous studies observed white matter alterations in the left posterior brain regions in adults and school‐age children with dyslexia. However, no study yet has examined the development of tract‐specific white matter pathways from the pre‐reading to the fluent reading stage in children at familial risk for dyslexia (FHD+) versus controls (FHD‐). This study examined white matter integrity at pre‐reading, beginning, and fluent reading stages cross‐sectionally (n = 78) and longitudinally (n = 45) using an automated fiber‐tract quantification method. Our findings depict white matter alterations and atypical lateralization of the arcuate fasciculus at the pre‐reading stage in FHD+ versus FHD‐ children. Moreover, we demonstrate faster white matter development in subsequent good versus poor readers and a positive association between white matter maturation and reading development using a longitudinal design. Additionally, the combination of white matter maturation, familial risk, and psychometric measures best predicted later reading abilities. Furthermore, within FHD+ children, subsequent good readers exhibited faster white matter development in the right superior longitudinal fasciculus compared with subsequent poor readers, suggesting a compensatory mechanism. Overall, our findings highlight the importance of white matter pathway maturation in the development of typical and atypical reading skills.
Investigations of Non-Physical Characteristic Modes of Material Bodies

Recently, researchers noticed that there are non-physical modes in characteristic modes of material bodies. In this paper, those non-physical modes are investigated. The reason for the non-physical modes is discussed. The influence of integral equations’ internal resonance on the non-physical modes are studied. It is concluded that the internal resonance is not responsible for the non-physical modes. Meanwhile, based on the extinction theorem, the dependent relationship between the equivalent surface electric and magnetic currents are proposed, and it is observed that the non-physical modes do not obey the dependent relationship, whereas the physical modes are governed by the dependent relationship. Therefore, it can be concluded that the lack of the dependent relationship causes the non-physical modes. Besides, based on the dependent relationship, a novel post-processing method to remove the non-physical modes is proposed. Numerical results of a dielectric cylinder are presented to validate the discussions and new post-processing method.
Effects of Crystal Orientation and Temperature on the Strength of Sapphire

The flexure and compressive strengths of sapphire are dependent on crystal orientation and temperature. Most notably, the c -axis compressive strength decreases below the tensile strength at temperatures >400°C and falls to 2% of the room-temperature compressive strength at 800°C. Loss of compressive strength complicates the interpretation of flexure tests. Four-point flexure specimens with no component of c -axis compression increase in strength at temperatures >500°C; however, specimens that have c -axis compression decrease in strength. It has been observed that c -axis compression causes twinning on rhombohedral crystal planes. Intersection of twins on different rhombohedral planes causes fracture that leads to mechanical failure.