Miracle-dz/UniFAR-FTUs huggingface dataset:
Progress toward a simplified polymerase chain reaction and its application to diagnosis of tuberculosis

The complexity, expense, and susceptibility to contamination of the polymerase chain reaction (PCR) are all issues which need to be overcome if PCR is to be used outside of research laboratories. We addressed these problems with respect to the diagnosis of tuberculosis. First, we simplified the procedure for extracting Mycobacterium tuberculosis DNA from sputum samples. Two methods of sample preparation were compared: the chaotrope-silica method and a novel, more simple chloroform method. Second, we developed a colorimetric method for product detection. This method was as sensitive and specific as agarose gel electrophoresis for detection of PCR product. By using a one-tube nested protocol, 5 to 50 genome equivalents of M. tuberculosis DNA were detected. The simplified colorimetric PCR was compared with microscopy and culture for detection of M. tuberculosis in clinical specimens of sputum. A total of 171 sputum samples were investigated from 108 patients, 12 of whom were subsequently found to have tuberculosis by culture and/or microscopy. PCR of samples prepared by the chaotrope-silica method had a sensitivity of 75% and a specificity of 100% whereas PCR of samples prepared by the chloroform method had a sensitivity of 92% and a specificity of 99% when compared with the sensitivities and specificities of the combined classical microbiological methods for the diagnosis of tuberculosis. The simplified colorimetric PCR in combination with the chloroform sample preparation method was at least as sensitive as microscopy but had a greater specificity because samples with atypical mycobacteria were not detected by PCR. The sensitivity of the method for detection of smear-negative and extrapulmonary tuberculosis remains to be investigated.
The More Things Change , the More They Stay the Same : Developing Countries ’ Unity in International Politics ∗

With the post-Cold War rise of major developing countries blurring the distinction between the industrialized “North” and the developing “South,” it is unclear whether a state’s development level remains a strong predictor of its stances in international politics. Do Brazil, India, China, South Africa, and other major developing countries behave like members of the North, or the South? And having been left behind in some respects, do other parts of the global South rally behind the major developing countries, or the North, or neither? Numerous scholars and practitioners claim that economic disparities fracture the traditional Southern coalition: major developing countries break ranks as their growing wealth links them more tightly to the countries, institutions, and policies associated with the North. Yet other observers insist that the Southern coalition is not only intact but strengthened. Instead of dissociating from the South, major developing countries leverage their growing power to defend poorer states and challenge richer ones – and perhaps poorer states are abandoning support for the North while unifying behind these new leaders. We lay out six observable implications that should be in place if the Southern coalition is intact. Then we probe those implications with statistical analyses of over 3,600 paragraphs of text from states’ negotiations concerning trade and environmental policy. This policy space facilitates generalizability by representing fundamental sovereignty and wealth issues that have been at the heart of friction between states at different levels of development. Our finding – that overall, developing countries have maintained remarkable unity – weighs in on central debates in international relations, comparative politics, and political economy. ∗For excellent research assistance or helpful comments, we thank Duke students Irina Danescu, Sanjeev Dasgupta, Margaret Foster, and Shanelle Van. For useful comments, we thank seminar audiences at the annual conferences of the International Studies Association (ISA) and the International Political Economy Society (IPES).
An Examination of Intellectual Capital and Corporate Financial Performance : Canonical Correlation Analysis

This study aims to examine the relationship between intellectual capital and corporate financial performance of Mobinil as an example of Egyptian telecom companies over sixteen years (from 1998 to 2013). The study identified three factors for intellectual capital as a first set of variables. They are structural capital, customer capital and human capital. Corporate financial performance variables represent the second set of the study which is earnings per share, earnings before interest, tax, depreciation and amortization (EBITDA) and revenue growth. To achieve the study’s objective, the study employs the Canonical correlation analysis as an appropriate statistical analysis. It analyses relationships between two sets of variables and maximises the correlation between linear composites of the intellectual capital and corporate performance variables. The findings of the study provide insights into the components of intellectual capital on an Egyptian Telecom Company and their influence on corporate financial performance. The Canonical correlation analysis provides evidence on a noteworthy relationship between intellectual capital, that is most influenced by customer capital and structural capital, and corporate financial performance that is most influenced by revenue growth and earnings per share. Furthermore this relationship was largely captured by the first two functions in the Canonical model. In conclusion, the results suggest that both customer capital and structural capital have a significant impact on corporate financial performance when measured by earnings per share and revenue growth, in contrast, human capital has no significant impact on corporate financial performance. Keywords*: Intellectual Capital; Corporate Financial Performance; Customer Capital; Human Capital; Structural Capital. 1 Definitions with all details for keywords are presented in section 2.1 in the paper.
Intracisternal A particle genes: Distribution in the mouse genome, active subtypes, and potential roles as species‐specific mediators of susceptibility to cancer

Rodents, mice and rats in particular, are the species of choice for evaluating chemical carcinogenesis. However, different species and strains often respond very differently, undermining the logic of extrapolation of animal results to humans and complicating risk assessment. Intracisternal A particles (IAPs), endogenous retroviral sequences, are an important class of transposable elements that induce genomic mutations and cell transformation by disrupting gene expression. Several lines of evidence support a role of IAPs as mouse‐specific genetic factors in responses to toxicity and expression of disease phenotypes. Since multiple subtypes and copies of IAPs are present in the mouse genome, their activity and locations relative to functional genes are of critical importance. This study identified the major “active” subtypes of IAPs (subtype 1/1a) that are responsible for newly transposed IAP insertions described in the literature, and confirmed that (1) polymorphisms for IAP insertions exist among different mouse strains and (2) promoter activity of the LTRs can be modulated by chemicals. This study further identified all the genes in the C57BL/6 mouse genome with IAP subtype 1 and 1a sequences inserted in their proximity, and the major biofunctional categories and cellular signaling networks of those genes. Since many “IAP‐associated genes” play important roles in the regulation of cell proliferation, cell cycle, and cell death, the associated IAPs, upon activation, can affect cellular responses to xenobiotics and disease processes, especially carcinogenesis. This systemic analysis provides a solid foundation for further investigations of the role of IAPs as species‐ and strain‐specific disease susceptibility factors. © 2009 Wiley‐Liss, Inc.
Specificity of the alteration in aldosterone biosynthesis in the spontaneously hypertensive rat.

The spontaneously hypertensive rat (SHR) has a decreased aldosterone response to angiotensin II (A II), resulting in a compensatory increase in the activity of the reninangiotensin system. To assess whether this is a selective or generalized defect in hormonal regulation, aldosterone responsiveness to two other secretagogues (ACTH and potassium) and the status of the pituitary-thyroidal and pituitary-adrenal axes were determined in three groups of rats: SHR, normotensive Kyoto-Wistar (WKY), and normotensive Sprague-Dawley rats (SDR). The rats were placed on either a low or a high sodium diet for 10 days, and then blood was obtained for the measurement of plasma aldosterone, corticosterone, A II, ACTH, TSH, T3, sodium, and potassium. Additionally, purified glomerulosa cells were incubated with increasing doses of either ACTH or potassium. No differences between the groups were observed in vivo for any of the parameters measured when the animals were on a high salt diet or for any on the low salt diet, exce.
DP 2017-04 The Labour Productivity Gap between Agricultural and Non-agricultural Sectors and Poverty in Asia *

The objective of this paper is to examine how agricultural and non-agricultural labour productivities have grown over time and whether the growth pattern – proxied by the labour productivity gap in two sectors – affected poverty in low and middle income countries in Asia. We first examine whether the labour productivities in agricultural and non-agricultural sectors have converged or not using a five-year average panel dataset. We have found evidence that non-agricultural labour productivity and agricultural labour productivity did not converge as the former has grown faster and the gap has increased significantly over time. We then confirm that both agricultural and non-agricultural labour productivities have converged across countries and the convergence effect is stronger for the non-agricultural sector. We have also observed that, despite the relatively lower growth in agricultural labour productivity, the agricultural sector played an important role in promoting non-agricultural labour productivity and thus in non-agricultural growth. Finally, we have found some evidence that the labour productivity gap reduces rural and urban poverty as well as the national inequality.
Validation of a modified Scoliosis Research Society instrument for patients with limb deformity: The limb deformity-Scoliosis Research Society (LD-SRS) score

Background: Despite the large negative effect of limb deformity on health-related quality of life (QoL), there exists no patient-reported instrument to quantify this impact. Rather, limb deformity research has been performed using global QoL measurements concurrently with joint-specific and/or arthritis outcome scales, thereby requiring the completion of multiple instruments. Furthermore, joint- and arthritis-specific instruments focus on the impact pain has on function, whereas limb deformities may be pain-free with greater social and functional impairment. The purpose of this study was to validate a patient-reported instrument to quantify limb deformity-related QoL. Materials and Methods: Because of the similarities with regard to pain, function, and body image between limb deformity and scoliosis, the Scoliosis Research Society-30 (SRS-30) spine deformity instrument was modified such that the words "back" and "trunk" were replaced with "limb" to create a novel instrument: the limb deformity-SRS (LD-SRS). Testing for construct validity (both convergent and discriminant), reliability, floor and ceiling effects, and minimal clinically important difference (MCID) was performed in a validation cohort of 62 subjects aged 18 years or older with nonarthritic, unilateral lower extremity deformity. Results: Scale reliability was excellent (test-retest reliability, intraclass correlation coefficient = 0.977; internal consistency, Cronbach′s alpha = 0.906), scores were normally distributed, and there were no floor or ceiling effects. There was also robust construct validity: convergent validity testing revealed positive correlations between the LD-SRS and all short-form-36 domains, the American Academy of Orthopaedic Surgeons-Lower Limb Module, and higher scores in those who were postcorrection. Discriminant validity was demonstrated with no correlations between the LD-SRS and subject age, sex, body mass index, surgeon-scored Limb Lengthening and Reconstruction Society-AIM Index, or surgeon-generated deformity measurements. MCID was calculated to be 0.3 (on a 4.0-point scale). Conclusions: The LD-SRS score is a reliable and valid instrument to measure limb deformity-related QoL in patients with nonarthritic lower extremity deformity. It is a valuable tool which allows clinicians to quantify patients′ deformity-related QoL with a single instrument, rather than repurposing scales which have been validated for other conditions and have limited applicability to the unique challenges of treating patients with a lower limb deformity. Level of Evidence: Diagnostic, Level 2.
CAST STEEL YIELDING FUSE FOR CONCENTRICALLY BRACED FRAMES

Since the construction of the distinct cable net roof structure of the 1972 Munich Olympic Stadium there has been a renaissance in the use of structural cast steel connections in buildings and bridges in Europe. More recently, the movement has crossed the ocean to North America. Although castings have been employed primarily in architecturally exposed structures where the cast elements and the structural members they are connected to are designed to remain elastic under all loading conditions, researchers have recently demonstrated that the freedom to control geometry and material properties makes steel castings an attractive solution for more severe loading conditions such as seismic-resistant connections for steel structures. This paper presents a new cast steel connector that acts as the energy dissipating element in a concentrically braced frame. Seismic energy is dissipated through inelastic flexural yielding of specially designed yielding elements of the cast connector. The cast connector concept is first introduced, the cast steel material used for a device prototype is then discussed and finally fullscale proof-of concept laboratory test results are presented.
Seed germination and conservation of two endemic species from Central Apennines ( Italy )

The Mediterranean mountains are one of the most threatened ecosystems in Europe, and endemic species are a significant feature of this environment. The definition of germination protocols for endemic, rare or threatened species is an important step for their conservation. The aim of this work was to analyze seed germination of Phyllolepidum rupestre Ten. Trinajstić and Crepis magellensis F. Conti & Uzunov, two endemic species growing in small populations in the Majella Nation Park (Central Apennines, Italy). The effects of temperature (5, 10, 15, 20, 25, 25/10 and 20/10°C), irradiance and gibberellic acid (250 and 500 ppm) on seeds germination were considered. A protocol for the in situ reintroduction was also developed. The results highlight a significant effect of temperature on seed germination. In particular, seed germination for P. rupestre and C. magellensis was 70.58 ± 3.75 % and 97.30 ± 3.13% at 20°C, respectively. These protocols can be used in reinforcement projects for wild populations.
Evaluation of selected bone metabolism markers in rheumatoid arthritis patients.

BACKGROUND Rheumatoid arthritis (RA) is a chronic systemic disease of connective tissue characterized by progressive destructive arthritis associated with deformation and impairment of the function of the motor system. RA patients more often present secondary osteoporosis and increased risk of fractures. The aetiology of the process remains not fully understood. A significant role is played by proinflammatory cytokines being common mediators of both inflammatory processes and bone remodelling. OBJECTIVES The purpose of the study was to evaluate the effect of activity of the inflammation and of applied therapy on osteogenesis marker concentrations in RA patients. MATERIAL AND METHODS Thirty six female patients with RA, confirmed according to ACR criteria, aged from 35 to 77 years were qualified into the study. A control group included 45 healthy women aged between 34 and 78 years. Clinical evaluation (number of painful and swollen joints, DAS 28) and evaluation of RA laboratory activity (ESR, CRP, blood cell count) and levels of selected bone metabolism markers (osteocalcin, PICP) and serum interleukin 1 levels were performed to carry out the study. X-rays of hands and densitometric scanning of the femoral bone neck and spine were completed in order to assess the advancement of lesions in the bones. RESULTS Osteocalcin and PICP levels were significantly lower in the RA groups compared to the control group (2.51 ± 0.22 pg/mL vs. 18.65 ± 12.84 pg/mL, p < 0.0001; 0.292 ± 0.047 pg/mL vs. 0.829 ± 0.263 pg/mL, p < 0.0001 respectively). A statistically significant difference was also observed between the levels of osteocalcin and PICP in both sub-groups of RA patients (DAS28 ≤ 5.1 and DAS28 > 5.1) and the control (osteocalcin 2.48 ± 0.23 pg/mL vs. 18.65 ± 12.84 pg/mL, p < 0.0001; 2.52 ± 0.22 pg/mL vs. 18.65 ± 12.84 pg/mL, p < 0.0001 respectively and PICP 0.281 ± 0.053 pg/mL vs. 0.829 ± 0.263 pg/mL, p < 0.0001; 0.298 ± 0.044 pg/mL vs. 0.829 ± 0.263 pg/mL, p < 0.0001 respectively). No correlation was demonstrated between the levels of selected bone metabolism markers and the therapy with methotrexate or cyclosporine. CONCLUSIONS Analysis of the obtained results confirms the presence of disorders of bone metabolism in RA patients. A chronic inflammatory process favors the development of osteoporosis in RA patients. Reduced levels of bone metabolism markers (osteocalcin, PICP) in the study group, compared to the control, may indicate a reduced pace of osteogenesis in RA patients. No effect of therapy with methotrexate and cyclosporine on bone metabolism in that group of patients was found.
An Optimized Seamless Dual-Link Handover Scheme for High-Speed Rail

In high-speed rail (HSR) with Long-Term Evolution (LTE) technology, the wireless communication quality of service (QoS) is enormously degraded because of the unstable signal and frequent handover. Recently, a seamless handover using two antennas on the top of a train has been introduced to provide a better user experience. The two antennas are mounted on the front and the rear of the train, respectively, so that one performs handover, and the other is communicating. A bicasting mechanism is adopted to eliminate the delay and overhead of data forwarding. In this paper, we consider a new algorithm to optimize the handoff opportunity by investigating not only the hysteresis exceeding level but the signal strength of both antennas as well. The parameter selection in the algorithm is analyzed based on a probability model. Furthermore, a set of new handover procedures, which optimize the utilization of the two antennas, is proposed to decrease the overhead and improve the QoS of the users. Accordingly, numerical results show that the handover failure probability (HFP) and the communication interruption probability (CIP) are both obviously reduced.
Attributing Oncogenic Human Papillomavirus Genotypes to High-grade Cervical Neoplasia: Which Type Causes the Lesion?

Human papillomavirus (HPV) is found in most women with high-grade cervical intraepithelial neoplasia (CIN) 2/3 in cervical cytology and biopsies. Multiple high-risk HPV (hrHPV) genotypes are present in 15% to 50% of cytology samples. We have shown by laser-capture microscopy (LCM)-polymerase chain reaction (PCR) that each lesion is associated with a single hrHPV type. Attribution of hrHPV types to CIN2/3 is important to understand the oncogenic role of different types and the limitations of cytologic typing. We studied hrHPV genotypes in 257 women with histologic CIN2/3 referred on the basis of abnormal cytology. HPV typing was done on cytology and CIN2/3 biopsies. If the whole-tissue section of the biopsy was positive for multiple hrHPV types, LCM-PCR was performed. We found 181 (70%) single and 71 (28%) multiple hrHPV infections in cytology, with 5 (2%) cases HPV-positive only on whole-tissue section PCR. Of cases with multiple cytologic hrHPV infections, 47/71 (66%) showed a single type in CIN2/3 lesions. In total, in 232 of 257 (90%) women with CIN2/3, a single hrHPV type caused CIN2/3. One was nonattributable on the LCM level. The remaining 24 women had 2 or more contiguous or separated lesions, each associated with a single hrHPV infection. The probability of HPV16 being present in CIN2/3, if detected in cytology, was 0.96 (95% confidence interval=0.90-0.98). LCM-PCR confirms that only 9% of histologic CIN2/3 is associated with multiple hrHPV types, much less than cytology would indicate, and each lesion was associated with a single hrHPV infection.
Performance of Reinforced Concrete Raft to Remedy ‘ Mushroom ’ Problem of Piled Embankment with Individual Pilecaps on Soft Ground

Piled embankment with individual pilecaps was constructed in the 1980’s as part of the expressway in the Northern State of Malaysia. The embankment is underlain by a thick layer of very soft compressible fine-grained soils. The original design principle of this solution was intended to rely solely on the arching of embankment materials to transfer load to pilecaps as the soft compressible subsoil between pilecaps settled under consolidation. However, a few years after the expressway was opened to traffic, the embankment continued to experience large differential settlement in the form of localised depressions that required regular maintenance and repaving. The depressions coincided with the area where there is no pilecap beneath the embankment. The protruding parts of the embankment at pilecaps with continuing settlement between pilecaps look like ‘mushroom’ and therefore the term is used to describe the problem. This paper presents an innovative method of using reinforced concrete (RC) raft near surface of the embankment to treat the problem and to prevent recurrence of differential settlement. A full-scale instrumented trial was carried out to verify the proposed remedial works. The instrumentation monitoring results of about two years are presented and discussed in this paper. The instrumentation results indicate that the reinforced concrete raft remedial measure is effective in reducing the total settlement and the differential settlement of the expressway embankment.
Design and Evaluation of a New Type of Knee Orthosis for Improving the Performance of Subjects with Knee Osteoarthritis

Knee joint osteoarthritis is a disease which influences the performance of the joint during walking. Various types of knee orthosis have been designed to improve the performance of the subjects, however they are not without problems. The aim of this paper is to design an orthosis which is easy to use and more economically efficient.Two subjects with knee osteoarthritis were recruited in this research study. The gait performance of the subjects and their stability while standing, were evaluated by use of motion analysis system and a force plate (Kistler). The mediolateral excursion of the knee joint decreased while walking with the knee orthosis in contrast to normal walking. Moreover, the adduction moment applied on the knee joint decreased significantly (p-value<0.05). The new design of the orthosis improves the performance of the subjects during walking. Moreover, it is more cosmesis, easy to use and more economically efficient.