Miracle-dz/UniFAR-FTUs huggingface dataset:
Hairpin structures are the primary amplification products: a novel mechanism for generation of inverted repeats during gene amplification

Early events of DNA amplification which occur during perturbed replication were studied by using simian virus 40 (SV40)-transformed Chinese hamster cells (CO60) as a model system. The amplification is observed shortly after carcinogen treatment, and the amplified sequences contain molecules organized as inverted repeats (IRs). SV40 amplification in vitro was studied by using extracts from carcinogen-treated CO60 cells. In the amplified DNA the SV40 origin region was rereplicated, while more distal sequences were not replicated even once. Using several experimental procedures such as sucrose gradients, "snap-back" assay, and two-dimensional gel electrophoresis, we show that the overreplicated DNA contains IRs which are synthesized de novo as hairpins or stem-loop structures which were detached from the template molecules. The fully replicated SV40 molecules synthesized by the HeLa extracts do not contain such IRs. We propose "U-turn replication" as a novel mechanism for gene amplification, accounting for the generation of extrachromosomal inverted duplications as a result of perturbed replication and template switching of the DNA polymerases.
R&D Intensity and Finance: Are Innovative Firms Financially Constrained?

The assumption of perfect capital markets is least likely to be satisfied for the class of firms which devote resources towards the development of innovative products or processes. Existing tests of the impact of capital market imperfections on innovative firms cannot distinguish between two alternative hypotheses: (i) that capital markets are perfect, and that different factors drive the firms different expenditures, and (ii) that capital markets are imperfect, and that the different expenditures of the firm respond disproportionately to a common factor, namely shocks to the supply of internal finance. However, an implication of the perfect capital markets assumption is that each of the firms expenditures should be equally insensitive to fluctuations in internal finance. Therefore, to distinguish between these hypotheses, the sensitivity of physical investment expenditures to internal finance is compared across innovative and non-innovative firms. For robustness, several investment equations are estimated. The results support the hypothesis that innovative firms are financially constrained.
Immediate Neurocognitive Effects of Concussion

OBJECTIVE To prospectively measure the immediate neurocognitive effects and early course of recovery from concussion and to examine the effects of loss of consciousness (LOC) and posttraumatic amnesia (PTA) on the severity of neurocognitive impairment immediately after concussion. METHODS A sports-related concussion research model was used to allow prospective immediate evaluation of concussion. A total of 2385 high school and college football players were studied. Ninety-one players (3.8%) sustained concussions during the study. A brief neurocognitive and neurological screening measure, the Standardized Assessment of Concussion, was used to assess cognitive functioning before the football season, immediately after injury, and 15 minutes, 48 hours, and 90 days after injury. RESULTS Standardized Assessment of Concussion scores immediately after concussion were significantly lower than the preseason baseline score and the noninjured population baseline mean, even for injured subjects without LOC or PTA. Subjects with LOC were most severely impaired immediately after injury, whereas those without LOC or PTA were least impaired. Significant impairment was also detected 15 minutes after injury, but all three groups returned to baseline levels of cognitive functioning within 48 hours. CONCLUSION These findings are the first to demonstrate not only that a gradient of increasing concussion severity is represented by PTA and LOC but also that measurable neurocognitive abnormalities are evident immediately after injury without PTA or LOC.
On the probability of perfection of software-based systems

The probability of perfection becomes of interest as the realization of its role in the reliability assessment of software-based systems. It is not only important on its own, but also in the reliability assessment of 1-out-of-2 diverse systems. By “perfection”, it means that thesoftware will never fail in a specific operating environment. If we assume that failures of a software system can occur if and only if it contains faults, then it means that the system is “fault-free”. Such perfection is possible for sufficiently simple software. While the perfection can never be certain, so the interest lies in claims for the probability of perfection. In this thesis, firstly two different probabilities of perfection – an objective parameter characterizing a population property and a subjective confidence in the perfection of the specific software of interest – are distinguished and discussed. Then a conservative Bayesian method is used to claim about probability of perfection from various types of evidence, i.e. failure-free testing evidence, process evidence and formal proof evidence. Also, a “quasiperfection” notion is realized as a potentially useful approach to cover some shortages of perfection models. A possible framework to incorporate the various models is discussed at the end. There are generally two themes in this thesis: tackling the failure dependence issue in the reliability assessment of 1-out-of-2 diverse systems at both aleatory and epistemic levels; and degrading the well-known difficulty of specifying complete Bayesian priors into reasoning with only partial priors. Both of them are solved at the price of conservatism. In summary, this thesis provides 3 parallel sets of (quasi-)perfection models which could be used individually as a conservative end-to-end argument that reasoning from various types of evidence to the reliability of a software-based system. Although in some cases models here are providing very conservative results, some ways are proposed of dealing with the excessive conservatism. In other cases, the very conservative results could serve as warnings/support to safety engineers/regulators in the face of claims based on reasoning that is less rigorous than the reasoning in this thesis.
PENGARUH STRUKTUR GOVERNANCE DAN ETNISITAS TERHADAP FEE AUDIT (STUDI PADA PERUSAHAAN YANG LISTING DI INDEKS KOMPAS 100

Abstrak Besar atau kecilnya fee audit menjadi perbincangan yang menarik, mengingat masih kurangnya riset mengenai faktor-faktor apa saja yang sebenarnya dapat memengaruhi besar kecilnya fee audit tersebut. Penelitian ini bertujuan untuk menguji apakah struktur governance yang diproksikan dengan independensi, ukuran, intensitas pertemuan dewan komisaris, keberadaan komite manajemen risiko serta independensi, ukuran, dan intensitas pertemuan komite audit menjadi faktor penentu besar kecilnya fee audit (professional fee). Selanjutnya penelitian ini juga menguji apakah variasi etnis pemilik perusahaan juga menjadi salah satu faktor penentu besar kecilnya fee audit, dimana etnis dipisahkan menjadi dua yaitu etnis masyarakat asli dan etnis masyarakat keturunan atau pendatang. Data yang digunakan merupakan data sekunder dari laporan keuangan perusahaan yang dipublikasikan . Jumlah perusahaan yang menjadi sampel dalam penelitian ini adalah sebanyak 78 perusahaan. Penelitian ini menggunakan teknik analsis data regresi berganda (multiple linier regression). Hasil pengujian menunjukan bahwa dari variabel-variabel yang diuji, terdapat empat variabel yang memberi pengaruh terhadap fee audit. keempat variabel tersebut antara lain dewan komisaris independen, komite manajemen risiko, komite audit independen, dan intensitas pertemuan komite audit. Kata Kunci : Dewan komisaris, komite Audit, etnisitas, fee audit Abstract In Indonesia, the size of the audit fee to be an interesting conversation, given the lack of research on what factors that could affect the size of the audit fee. This study aimed to test whether the governance structure that is proxied to the independence, the size, the intensity of the board meeting, the existence and independence of the risk management committee, size, and intensity of audit committee meetings be the deciding factor on the size of audit fees (professional fee). Furthermore, this study also examined whether ethnic variation owner of the company also became one of the factors determining the size of the audit fee, which is separated into two ethnic ethnicity indigenous and ethnic descent communities or immigrants. The data used are secondary data from published financial statements . The number of companies that were visited in this study were as many as 78 companies. This study uses the technique of multiple regression analysis is the data (multiple linear regression). The test results showed that of the variables tested, there are four variables that influence the audit fee. four variables include an independent board of directors, risk management committee, an independent audit committee, and the intensity of audit committee meetings. Keywords: Board of Commissioners, the Audit Committee, ethnicity, audit fee
Is advanced technical functionality enough? - Value creation in a complex warehouse management system investment : Lessons learned about the implication of resources, roles and interactions

Supply chain management complexity is a growing challenge for a broad range of contemporary companies, which makes them turn to new and increasingly advanced IT-systems as a salvation. One of the currently most important system in a supply chain manager’s toolbox is the warehouse management system. As business challenges increases so does also the complexity in the investment processes surrounding the warehouse management systems, this paper explores value creation in these processes to understand the resource exchanges involved, the exchange actor’s different roles and the implications of interactions between the actors. This is conducted through a case study with a market leading warehouse management system vendor and a supply chain intensive customer.The findings indicate that value creation in a complex warehouse management system investment entails several intervened and ongoing processes of different resource exchanges, were the actors co-create value jointly by sharing, combining and utilizing the resources throughout these processes. In order to establish this essential value co-creation sphere, also social exchanges in the form of qualitative interactions between the actors have proven to be a fundamental factor.
Computing and the Step Function

One aspect of the engineering education that the author began back in the early 1950's seemed very strange at the time. It was the serious consideration of the step function, which was unlike anything treated in highschool mathermatics because it was discontinuous. While its relevance to the design of mechanical and electrical machinery soon became obvious, it has recently occurred to the author that the step function is just as relevant to the use of machinery, in particular, computers. The engineering problem is that x is usually a value of time, thus the step function requires an instantaneous change from y' to y". In spatial terms, this is an indefinitely large acceleration. In mechanical terms, it means an indefinitely large force. These are unnatural and, in physical systems at least, neither an input nor an output can be exactly stepped. The engineering challenge is to take an input that's practically a step function and give an output that can be used as a step function, sometimes after cleaning it up. In digital circuitry, the square waves that encode bits in transmission are ideally a sequence of step functions, and the bit rate is limited by the distortion during transmission.
Quality of Life Questionnaire-Bronchiectasis: final psychometric analyses and determination of minimal important difference scores

Background The Quality of Life-Bronchiectasis (QOL-B), a self-administered, patient-reported outcome measure assessing symptoms, functioning and health-related quality of life for patients with non-cystic fibrosis (CF) bronchiectasis, contains 37 items on 8 scales (Respiratory Symptoms, Physical, Role, Emotional and Social Functioning, Vitality, Health Perceptions and Treatment Burden). Methods Psychometric analyses of QOL-B V.3. 0 used data from two double-blind, multicentre, randomised, placebo-controlled, phase III trials of aztreonam for inhalation solution (AZLI) in 542 patients with non-CF bronchiectasis and Gram-negative endobronchial infection. Results Excellent internal consistency (Cronbach's α ≥0.70) and 2-week test–retest reliability (intraclass correlation coefficients ≥0.72) were demonstrated for each scale. Convergent validity with 6 min walk test was observed for Physical and Role Functioning scores. No floor or ceiling effects (baseline scores of 0 or 100) were found for the Respiratory Symptoms scale (primary endpoint of trials). Baseline Respiratory Symptoms scores discriminated between patients based on baseline FEV1% predicted in only one trial. The minimal important difference score for the Respiratory Symptoms scale was 8.0 points. AZLI did not show efficacy in the two phase III trials. QOL-B responsivity to treatment was assessed by examining changes from baseline QOL-B scores at study visits at which protocol-defined pulmonary exacerbations were reported. Mean Respiratory Symptoms scores decreased 14.0 and 14.2 points from baseline for placebo-treated and AZLI-treated patients with exacerbations, indicating that worsening respiratory symptoms were reflected in clinically meaningful changes in QOL-B scores. Conclusions Previously established content validity, reliability and responsivity of the QOL-B are confirmed by this final validation study. The QOL-B is available for use in clinical trials and routine clinical practice.
A Structural Approach for Predicting Default Correlation

Default correlation is a critical concept in risk management for fixed income investment, bank management, and insurance industry, working capital management, among many. We extend the Leland-Toft term structure model into a two-firm environment and predict the default correlation between two firms by directly simulating the calibrate model based on the observed equity data (1990-2010) for various ratings. Using our empirical default correlation estimation as the benchmark, our investigation sheds more light on the structural approach in predicting default correlation. The results show that our approach outperforms the previous Zhou’s model, thereby our approach is not only theoretical improvement, but also has an empirical advantage.
Attitude of the Canine in Secondary Bone-Grafted and Nongrafted Patients with Cleft Lip and Palate

Objective To investigate the eruption pattern of the cleft-side canine regarding its pre-eruption position relative to the cleft in bone-grafted (BG) and nongrafted (NonBG) patients with cleft lip and palate. Methods Fifty-three patients with cleft lip and palate (21 BG, 32 NonBG) were examined by panoramic radiography and posteroanterior cephalography taken before and after canine eruption. Subjects were categorized into BG, NonBG, and control groups. Canines at the pre-eruption stage were categorized as close to (group 1) or distant from (group 2) the cleft area. The canine angle and its change between the two stages were evaluated. Results No significant differences were noted between the initial canine angle of the BG and NonBG groups. Although canines in the BG group erupted without a significant change in angle, the canine angle increased significantly (p < .0001) in the NonBG and control groups. In group 1, a greater change in canine angle was noted in the NonBG (p < .05) and control (p < .01) groups than in the BG group. In group 2, no significant difference was noted among the three groups. Conclusions In BG patients, a canine located near the cleft appears to erupt at the same angle as it had before grafting. However, in NonBG patients, it erupts more vertically, guided by cortical bone. For canines distant from the cleft area, there is no significant difference in the change in angulation between NonBG and BG patients.
The Commitment of Finance, Duplicated Monitoring and the Investment Horizon

The paper presents a simple model of financial contracting for a long-term investment project in which early project termination may be an optimal response to information asymmetries. The paper characterizes when this constellation leads to inefficient short- term investment. It is shown that in this setting delegated monitoring is problematic because it creates a commitment problem for the investor. This yields a countervailing effect to the scale economies inherent in the delegation of monitoring. It is shown that contracting with more than one investor can provide an informational insurance to the firm which lengthens its planning horizon.
Handedness- and Brain Size-Related Efficiency Differences in Small-World Brain Networks: A Resting-State Functional Magnetic Resonance Imaging Study

The human brain has been described as a complex network, which integrates information with high efficiency. However, the relationships between the efficiency of human brain functional networks and handedness and brain size remain unclear. Twenty-one left-handed and 32 right-handed healthy subjects underwent a resting-state functional magnetic resonance imaging scan. The whole brain functional networks were constructed by thresholding Pearson correlation matrices of 90 cortical and subcortical regions. Graph theory-based methods were employed to further analyze their topological properties. As expected, all participants demonstrated small-world topology, suggesting a highly efficient topological structure. Furthermore, we found that smaller brains showed higher local efficiency, whereas larger brains showed higher global efficiency, reflecting a suitable efficiency balance between local specialization and global integration of brain functional activity. Compared with right-handers, significant alterations in nodal efficiency were revealed in left-handers, involving the anterior and median cingulate gyrus, middle temporal gyrus, angular gyrus, and amygdala. Our findings indicated that the functional network organization in the human brain was associated with handedness and brain size.
Fluorescence of native single‐Trp mutants in the lactose permease from Escherichia coli: Structural properties and evidence for a substrate‐induced conformational change

Six single‐Trp mutants were engineered by individually reintroducing each of the native Trp residues into a functional lactose permease mutant devoid of Trp (Trp‐less permease; Menezes ME, Roepe PD, Kaback HR, 1990, Proc Natl Acad Sci USA 87:1638–1642), and fluorescent properties were studied with respect to solvent accessibility, as well as alterations produced by ligand binding. The emission of Trp 33, Trp 78, Trp 171, and Trp 233 is strongly quenched by both acrylamide and iodide, whereas Trp 151 and Trp 10 display a decrease in fluorescence in the presence of acrylamide only and no quenching by iodide. Of the six single‐Trp mutants, only Trp 33 exhibits a significant change in fluorescence (ca. 30% enhancement) in the presence of the substrate analog β,D‐galactopyranosyl 1‐thio‐β,D‐galactopyranoside (TDG). This effect was further characterized by site‐directed fluorescent studies with purified single‐Cys W33 → C permease labeled with 2‐(4′‐maleimidylanilino)‐naphthalene‐6‐sulfonic acid (MIANS). Titration of the change in the fluorescence spectrum reveals a 30% enhancement accompanied with a 5‐nm blue shift in the emission maximum, and single exponential behavior with an apparent KD of 71 μM. The effect of substrate binding on the rate of MIANS labeling of single‐Cys 33 permease was measured in addition to iodide and acrylamide quenching of the MIANS‐labeled protein. Complete blockade of labeling is observed in the presence of TDG, as well as a 30% decrease in accessibility to iodide with no change in acrylamide quenching. Overall, the findings are consistent with the proposal (Wu J, Frillingos S, Kaback HR, 1995a, Biochemistry 34:8257–8263) that ligand binding induces a conformational change at the C‐terminus of helix I such that Pro 28 and Pro 31, which are on one face, become more accessible to solvent, whereas Trp 33, which is on the opposite face, becomes less accessible to the aqueous phase. The findings regarding accessibility to collisional quenchers are also consistent with the predicted topology of the six native Trp residues in the permease.
Primary bone marrow lymphoma is a rare neoplasm with poor outcome: case series from single tertiary care centre and review of literature

Primary bone marrow lymphoma is a rare disease and remains undiagnosed due to deceptive clinical presentation. Here, we report four cases of primary bone marrow B‐cell non‐Hodgkin lymphoma, which presented with cytopenias without any lymphadenopathy or organomegaly. Bone marrow examination revealed large atypical B‐cells with a reactive T‐cell infiltrate with suppression of the normal hematopoietic elements. This lymphoma is known to have a poor prognosis. Inspite of treatment, two of our patients died during chemotherapy. Two patients relapsed, of which one showed an early relapse after two months and was put on an alternative regimen. The other patient relapsed twice at an interval of 4 and 5 years, respectively, following which he remained in remission for another 5 years and had recently shown a relapse for the third time. Review of literature revealed seven case series and 11 case reports of primary bone marrow lymphoma in the last five decades.
Recent methodological approaches in ethnographies of human and non-human Amerindian collectives

Abstract I examine recent ethnographic attempts to address alterity among Amerindian worlds—attempts that produce a critique of indigenous relationships with external or foreign agents. While some of them are concerned with describing what there is in those worlds, others illustrate different forms to approach it. The former studies carry out their descriptions through two contrasted types of fieldwork data: abstract indigenous concepts and material things. The latter studies are examined as illustrations of differentiated methodological advances: on the one hand, a writing experiment proposing an avant-garde engaged unruly ethnography; and on the other hand, what seems to be a mere accommodation of academic theoretical trends. The final picture of these current anthropological ethnographies depicts the contrasted contents and forms that are nowadays present in Amerindian studies.
Major gene with sex‐specific effects influences fat mass in Mexican Americans

Increased adiposity has repeatedly been identified as a major risk factor for a variety of chronic diseases. However, the question still remains whether the amount of adipose tissue itself is genetically mediated. To address this question, a segregation analysis, using maximum likelihood techniques as implemented in the computer program Pedigree Analysis Package (PAP), was performed on fat mass (kilograms of body fat) in a large sample of extended Mexican American families residing in San Antonio, TX. The only model not rejected was a Mendelian mixed model for fat mass, incorporating genotype X sex interaction. In males the major gene accounted for 37% of the total variance compared with 43% in females. In both sexes homozygous recessive individuals have a fat mass more than double that of individuals of the other two genotypes. It was possible to reject linkage of the anonymous major gene for fat mass with several candidate loci for obesity. However, tentative evidence of linkage was detected with markers on both chromosomes 2 and 11, thereby providing hypotheses for future testing. ©1995 Wiley‐Liss, Inc.