Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Worst Case Complexity of the k-means Method

The k-means method is an old but popular clustering algorithm known for its speed and simplicity. Until recently, however, no meaningful theoretical bounds were known on its running time. In this paper, we demonstrate that the worst-case running time of k-means is superpolynomial by improving the best known lower bound from $\Omega(n)$ iterations to $2^{\Omega(\sqrt{n})}$. To complement this lower bound, we show a smoothed-analysis type polynomial time upper bound for k-means.
Positions statement: criteria for defining polycystic ovary syndrome as a predominantly hyperandrogenic syndrome: an Androgen Excess Society guideline.

OBJECTIVE The Androgen Excess Society (AES) charged a task force to review all available data and recommend an evidence-based definition for polycystic ovary syndrome (PCOS), whether already in use or not, to guide clinical diagnosis and future research. PARTICIPANTS Participants included expert investigators in the field. EVIDENCE Based on a systematic review of the published peer-reviewed medical literature, by querying MEDLINE databases, we tried to identify studies evaluating the epidemiology or phenotypic aspects of PCOS. CONSENSUS PROCESS The task force drafted the initial report, following a consensus process via electronic communication, which was then reviewed and critiqued by the AES Board of Directors. No section was finalized until all members were satisfied with the contents and minority opinions noted. Statements that were not supported by peer-reviewed evidence were not included. CONCLUSIONS Based on the available data, it is the view of the AES Task Force on the Phenotype of PCOS that there should be acceptance of the original 1990 National Institutes of Health criteria with some modifications, taking into consideration the concerns expressed in the proceedings of the 2003 Rotterdam conference. A principal conclusion was that PCOS should be first considered a disorder of androgen excess or hyperandrogenism, although a minority considered the possibility that there may be forms of PCOS without overt evidence of hyperandrogenism but recognized that more data are required before validating this supposition. Finally, the task force recognized, and fully expects, that the definition of this syndrome will evolve over time to incorporate new research findings.
IN VITRO CLONAL PROPAGATION THROUGH DIRECT SHOOT ORGANOGENESIS OF THYMUS BROUSSONETII - A VULNERABLE AROMATIC AND MEDICINAL PLANT SPECIES

This paper reports, for the first time, a rapid and reliable micropropagation protocol for high-frequency shoot regeneration and plant establishment of Thymus broussonetii, a vulnerable and highly valuable aromatic and medicinal plant. This plant species is threatened by over collection due to its socioeconomic importance. Hence, an attempt has been made for in vitro cultivation of this plant for large scale multiplication as well as conservation. Several treatments such as cytokinin types and concentrations, cytokinin/auxin ratio, gelling agents, and explant density were tested on the shoot bud induction. Effects of various concentrations of auxins were also examined on the micropropagated shoots during rooting stage. Full- strength Murashige and Skoog (MS) medium supplemented with 6- benzylaminopurine (4.4 µM) and naphthalene acetic acid (1 µM) promoted significantly shoot bud induction while affecting shoot length. The use of 3 g/l of gellan gum (Phytagel™) promoted shoot bud induction and growth. For micropropagated shoot rooting, hormone-free MS medium exhibited the best results. The micropropagated plantlets were successfully hardened and 94% of them were found healthy after transplantation to ex vitro conditions. The micropropagated plants established in soil showed normal flowering did not show any morphological abnormality during one year of growth.
Transfer of plasmids pBR322 and pBR325 in wastewater from laboratory strains of Escherichia coli to bacteria indigenous to the waste disposal system

Laboratory strains of Escherichia coli containing plasmid pBR325 (or pBR322) were coincubated with a mobilizer strain of E. coli (containing the conjugative plasmid R100-1) and a recipient strain of bacteria. Bacterial strains isolated from raw wastewater or a plasmid-free E. coli laboratory strain served as recipients. Transfer of the pBR plasmid into the recipient strain occurred during a 25-h coincubation in either L broth or sterilized wastewater; transfer frequencies were several orders of magnitude lower in wastewater. After the coincubation, recipients exhibited both plasmid-encoded phenotypic characteristics and an altered plasmid profile, as shown by agarose gel electrophoresis of purified plasmid DNA.
Can Psychosocial Intervention Improve Peer and Sibling Relations Among War‐affected Children? Impact and Mediating Analyses in a Randomized Controlled Trial

Social resources are considered important protectors in traumatic conditions, but few studies have analyzed their role in psychosocial interventions among war-affected children. We examined (1) whether a psychosocial intervention (teaching recovery techniques, TRT) is effective in improving peer and sibling relations, and (2) whether these potentially improved relations mediate the intervention's impacts on children's mental health. Participants were 428 Palestinian children [10–13 (mean = 11.29, standard deviation SD = .68)-year-old girls (49.4 percent) and boys (50.6 percent)], who were cluster-randomized into the TRT and wait-list control groups. They reported the quality of peer (friendship and loneliness) and sibling (intimacy, warmth, conflict, and rivalry) relations, and posttraumatic stress, depressive and psychological distress symptoms, as well as psychosocial well-being at baseline (T1), postintervention (T2), and six month follow-up (T3). Results showed gender-specific TRT intervention effects: Loneliness in peer relations reduced among boys and sibling rivalry reduced among girls. The TRT prevented the increase in sibling conflict that happened in the control group. The mediating hypothesis was partially substantiated for improved peer relations, and beneficial changes in sibling relations were generally associated with improved mental health.
Affected‐only multiplex pedigree analysis of GAW10 problem 2

From a single extended pedigree simulation replicate, high density, affected only subpedigrees were isolated, based on the T > 40 affected status for the disease trait, Q1. On this sample of 14 pedigrees, with a range of two to six affected members (48 total), we conducted a haplotype based, multilocus, nonparametric genome‐wide search of the provided data (367 markers) using the computer program GENEHUNTER. As with most genome screens in complex diseases, the objective of this strategy was to identify regions (hot‐spots) which breached our predetermined threshold (p < 0.05), requiring confirmation by other groups or consortia. Of the six regions with threshold breaching scores (p < 0.05), the most promising, on chromosome 8 and chromosome 4, corresponded to the locations of MG2 and MG3. Both of these regions have multiple, consecutive markers above threshold and contained the only scores that exceeded p < 0.01. In addition, a fourth hot‐spot consisting of a single marker above threshold, was less than 15 cm from MG1 on chromosome 5. The positions of the remaining three hot‐spots did not correspond to the any of the major genes and are therefore false positives. An additional analysis of a single nuclear pedigree simulation replicate, using the extended transmission disequilibrium test (ETDT), was applied to markers in each of the above hot‐spot regions to look for evidence of disequilibrium with the disease trait. This analysis provided weak additional support for the chromosome 8 finding, even though the sample was very small (36 pedigrees containing 44 affected offspring). © 1997 Wiley‐Liss, Inc.
Output feedback robust adaptive controller design for dynamic atomic force microscopy

This paper analyzes the dynamics of amplitude modulation atomic force microscope (AM-AFM) which is the mostly employed mode in current AFMs. A reduced model is proposed to approximate the function of tip-sample separation to oscillation amplitude. Considering the fact that the model parameters vary with different combinations of piezo-scanner and cantilever as well as the measured sample, a robust adaptive controller is designed to reduce the system regulation error. Specifically, by using the K-filter, an observer is designed firstly for this output feedback problem. Based on this observer, we design a robust adaptive controller consisting of two parts: an adaptive component is used to deal with the unknown parameters, while the model uncertainty and system disturbance are accounted for by a robust control part. With the aid of Lyapunov technique, the stability of this control method is guaranteed and GUUB result is obtained. Additionally, the attractive region is analyzed particularly in the case of measurement saturation which usually occurs in dynamic AFM mode. To verify its effectiveness, some simulation results are included to show the performance of the proposed control strategy.
[Prospective randomized trial of optimum anal canal release treatment for chronic anal fissure].

4 刘凤斌 , 赵 利 . 建立中医疗效测评量表体系研究的设 想[ J] . 中国临床康复 , 2004 , 8 (1 ) : 164-165 . 5 郭新峰 , 赖世隆 , 梁伟雄 . 中医药临床疗效评价中结局 指标的选择与应用 [ J ] . 广州中医药大学学报 , 2002 , 19( 4) : 251-255 . 6 Fleming TR , DeMets DL . Surrogate end poin ts in clinical tr ials : are we being mislead ? [ J ] . Ann Inte rn Med , 1996 , 125( 7) : 605-613 . 7 赖世隆 , 胡镜清 , 郭新峰 . 循证医学与中医药临床研究 [ J] . 广州中医药大学学报 , 2000 , 17(1 ) : 1-8 . 8 宋 军 , 陈可冀 . 中医药临床疗效评价若干问题思考 [ J] . 中国中西医结合杂志 , 2003 , 23(8 ) : 564-565 . 9 徐 燕 , 徐厚谦 . 用循证医学方法提高中医药临床科研 质量 [ J ] . 甘肃中医学院学报 , 2003 , 20(4 ) : 20-21 . [收稿日期 ] 2004-12-24 [本文编辑] 周庆辉
Computational Constancy Measures of Texts—Yule’s K and Rényi’s Entropy

This article presents a mathematical and empirical verification of computational constancy measures for natural language text. A constancy measure characterizes a given text by having an invariant value for any size larger than a certain amount. The study of such measures has a 70-year history dating back to Yule's K, with the original intended application of author identification. We examine various measures proposed since Yule and reconsider reports made so far, thus overviewing the study of constancy measures. We then explain how K is essentially equivalent to an approximation of the second-order Rényi entropy, thus indicating its signification within language science. We then empirically examine constancy measure candidates within this new, broader context. The approximated higher-order entropy exhibits stable convergence across different languages and kinds of text. We also show, however, that it cannot identify authors, contrary to Yule's intention. Lastly, we apply K to two unknown scripts, the Voynich manuscript and Rongorongo, and show how the results support previous hypotheses about these scripts.
Two Sample Comparison based on Semi-Competing Risks Data

Semi-competing risks data are commonly seen in biomedical applications. In this article, we consider the problem of two-sample comparison based on a non-terminal event, say disease progression, which is subject to censoring by a terminal event such as death. Existence of possible dependent censoring complicates the analysis. The proposed methodology is developed under two types of assumptions. First, separate copula models are assumed for the two groups and then a flexible model measuring the group difference is imposed on the progression time. A competing approach for estimating the groupdifference parameter is the method proposed by Lin et al. (1996) which requires making additional marginal assumption on the terminal event and implicitly assumes that the dependence structures in the two groups are the same. Although here we put an extra copula assumption on the observable region, we also propose a model checking approach to assess its validity. Via simulations, we compare the two competing methods based on their finite-sample performances and robustness properties if the imposed assumptions are violated. The proposed method is applied to a data set of bone marrow transplant provided in Klein and Moeschberger (2003).
Analysis of low complex region peptides derived from mollusk shell matrix proteins using CID, high‐energy collisional dissociation, and electron transfer dissociation on an LTQ‐orbitrap: Implications for peptide to spectrum match

Identification of proteins involved in mollusk biomineralization by proteomics approach is gaining importance. These proteins are often characterized by low‐complexity regions (LCRs) made of repeating motifs that are constituted by few amino acids (e.g. IGG, DD, KK, and GGG). In this work, we have analyzed the fragmentation of model LCR peptides under different fragmentation regimes (CID, high‐energy collisional dissociation [HCD], and electron transfer dissociation [ETD]) and its consequences on peptide to spectrum matches (PSMs) using two search algorithms (Mascot and PEAKS DB). For both search tools, higher number of PSMs was obtained using CID spectra, followed by HCD and ETD. Intense fragment ions present in the lower m/z region of HCD led to lower PSM scores and absence of low mass cut off seems to offer little advantage for the identification of LCR peptides. Generally, doubly charged peptides under ETD conditions did not fragment to yield sequence information rich spectra. The spectral quality is affected by the nature of the repeating motifs in the peptide. The performance of both Mascot and PEAKS DB (de novo based search tool) vary according to the fragment regime employed to acquire MS/MS spectra.
A Self Contained Recorder For Acoustic Observations from AUV's

An experiment to acoustically observe baleen whale vocalizations from autonomous underwater vehicles (AUV's) in the southwestern Gulf of Maine was conducted in May of 2005. A digital recorder and hydrophone were installed on three Slocum Electric Gliders, which have the desirable features of a low acoustic signature and the ability to persistently keep station. To adequately identify whale vocalizations, the recorders combined fidelity (a combination of sampling frequency and bit depth) and unit-to-unit clock accuracy, for determining source location by using time of arrival triangulation. A fourth glider was configured with an ADCP. All four gliders were also outfitted with conductivity, temperature, depth, and bio-optical sensors. They were programmed to keep station 5-7 km apart in an approximate equilateral formation. The recorders were installed internally with a bottom-mounted hydrodynamic-shaped hydrophone. The electronics were electrically isolated from the glider and designed to be started and stopped in response to the passage of a magnet near a section of the hull. Each recorder, powered by a 10 'C' cell battery pack and using a 4 GB compact FLASH card, can thus store a single channel linear encoded 16-bit audio signal, sampled at 2048 Hz for 12 days. A module was designed and built to synchronize the ultra stable temperature tracking real time clocks. By using spectrogram cross correlation of the acoustic data, and estimates of the glider location, whale positions were determined with an accuracy of a few hundred meters
Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions

Summary Cytochrome P450 monooxygenases are useful biocatalysts for C–H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations.
Fault Detection and Diagnosis in IP-Based Mission Critical Industrial Process Control Networks

Mission-critical industrial process control networks support secure and reliable communications of devices in a controlling or manufacturing environment. They used to mostly use proprietary protocols and networks. Recently, however, many of them are being migrated to IP-based networks to consolidate many different types of networks into a single common network to simplify network operation, administration, and maintenance, and reduce operational expenses and capital expenditures. Despite their wide deployment, most operators have very little knowledge on how to operate them reliably and securely. This is mainly due to the operators' unfamiliarity with various faults that occur on IP-based process control networks. The current process of detecting and diagnosing faults in process control networks is mostly manual and thus the operators detect the problems only after noticeable process malfunctions. This article presents an overview of industrial process control networks and discusses the issues of introducing IP technologies into them. We then propose a fault detection and diagnosis method which is suitable for IP-based process control networks. We also present the system architecture and implementation of fault detection and diagnosis system as well as its deployment at POSCO. Finally, based on operational experience, we have generated a failure prediction model that can be used to predict potential alarms.
Rationing Capacity in Advance Selling to Signal Quality

We consider a seller who can sell her product over two periods, advance and spot. The seller has private information about the product quality, which is unknown to customers in advance and publicly revealed in spot. The question we consider is whether the seller has an incentive to signal quality in advance and, if so, how she can convey a credible signal of product quality. We characterize the seller's signaling strategy and find that rationing of capacity in the advance period is an effective tool of signaling product quality. We find that the high-quality seller can distinguish herself by allocating less capacity than the low-quality seller in the advance period. We show that this signaling mechanism exists whenever advance selling would be optimal for both the high-quality and low-quality sellers if quality were known by the consumers. Interestingly, the seller's ability to ration rationing flexibility sometimes disadvantages the seller; this effect is independent of product quality. This paper was accepted by Yossi Aviv, operations management.
Nonprofit organizations in the health sector.

Government appears to both promote and mistrust nonprofit organizations in the health sector. Tax exemptions, subsidies, and preferential treatment in contracts support these organizations. Legislation that links the supply of charity care to tax exemptions demonstrates mistrust. In this paper, the authors argue that information asymmetries lie at the heart of the current discomfort with tax policy toward nonprofit health-care providers. The authors examine current policy in terms of the rationale for the exemption of nonprofit health-care organizations from taxes as well as the ability of government to monitor performance of these organizations.
SDSS Imaging Pipelines

The SDSS project has taken 5-band data covering approximately 3000 deg2, or 4Tby of data. This has been processed through a set of image-processing pipelines, and the resulting catalogues of about 100 million objects have been used for a number of scientific projects. We discuss our software infrastructure, and outline the architecture of the SDSS image processing pipelines. In order to process this volume of data the pipelines have to be robust and reasonably fast; because we have been interested in looking for rare objects, the number of outliers due to deficiencies in the data and bugs in the software must be small. We have found that writing the codes has been one of the harder and more expensive aspects of the entire survey.
Modeling and Verification of Zone Controller: The SCADE Experience in China's Railway Systems

Communications Based Train Control (CBTC) is the newest railway system to solve traffic congestion in China's cities. Compared with the traditional signaling systems, CBTC systems are more complicated for which the modern moving block systems have been designed so that the exact position of a train can be known more accurately. Using traditional software development processes to design and expand such large systems are costly, and become unsustainable. Safety-critical application development environment (SCADE) is the systemic solution for developing critical systems. It fulfills the requirement of design, simulation, verification and automatic code generation of safety critical systems as CBTC. However, modeling and verifying CBTC is still a challenging problem. According to our experience in modeling and verifying the Zone Controller (ZC) of CBTC, the SCADE based development process does not reduce the complexity of large systems, which leads to verification failure. Therefore, improving the SCADE based development process is an urgent task. In this work, the slicing criteria that the SCADE process must conduct in order to simplify the complexity of SCADE models are stated. For each type of observer in SCADE, examples of available slicing criteria are given and their effects on reducing state space are analyzed. Finally, as a practical example, ZC is modeled and verified by SCADE using the slicing criteria.