Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyzing the catalytic role of Asp97 in the methionine aminopeptidase from Escherichia coli

An active site aspartate residue, Asp97, in the methionine aminopeptidase (MetAPs) from Escherichia coli (EcMetAP‐I) was mutated to alanine, glutamate, and asparagine. Asp97 is the lone carboxylate residue bound to the crystallographically determined second metal‐binding site in EcMetAP‐I. These mutant EcMetAP‐I enzymes have been kinetically and spectroscopically characterized. Inductively coupled plasma–atomic emission spectroscopy analysis revealed that 1.0 ± 0.1 equivalents of cobalt were associated with each of the Asp97‐mutated EcMetAP‐Is. The effect on activity after altering Asp97 to alanine, glutamate or asparagine is, in general, due to a ∼ 9000‐fold decrease in kca towards Met‐Gly‐Met‐Met as compared to the wild‐type enzyme. The Co(II) d–d spectra for wild‐type, D97E and D97A EcMetAP‐I exhibited very little difference in form, in each case, between the monocobalt(II) and dicobalt(II) EcMetAP‐I, and only a doubling of intensity was observed upon addition of a second Co(II) ion. In contrast, the electronic absorption spectra of [Co_(D97N EcMetAP‐I)] and [CoCo(D97N EcMetAP‐I)] were distinct, as were the EPR spectra. On the basis of the observed molar absorptivities, the Co(II) ions binding to the D97E, D97A and D97N EcMetAP‐I active sites are pentacoordinate. Combination of these data suggests that mutating the only nonbridging ligand in the second divalent metal‐binding site in MetAPs to an alanine, which effectively removes the ability of the enzyme to form a dinuclear site, provides a MetAP enzyme that retains catalytic activity, albeit at extremely low levels. Although mononuclear MetAPs are active, the physiologically relevant form of the enzyme is probably dinuclear, given that the majority of the data reported to date are consistent with weak cooperative binding.
A Community-Based Participatory Approach to Youth Development and School Climate Change: The Alignment Enhanced Services Project

Background: School–community partnerships offer an opportunity to promote positive youth development. However, there is a need for community-based participatory research (CBPR) models that leverage community and school resources to create environments that support youths' success.Objective: Describe the CBPR process used by Alignment Enhanced Services (AES) partners to develop and implement a strategy to promote a positive school climate, and to discuss factors that influence the AES process in the schools.Methods: A committee of school and community members developed the AES process, which included an environmental scan that solicited input from internal and external stake-holders on the schools' assets and needs related to youth development and school climate. AES coordinators, in consultation with school administrators, developed and implemented action plans that leveraged each school's existing strengths, while identifying and utilizing new resources to address systemic and individual needs.Lessons Learned: To date, the project has produced encouraging results; however, the AES process resulted in numerous challenges for the coordinators, schools, and community partners.Conclusion: AES offers a method for engaging the stakeholders in addressing critical issues related to youth development and school climate.
Joint Cell Zooming and Channel Allocation Using C-SAP for Large Action Sets

Optimizing energy consumption is paramount to sustain the growth of cellular networks. One of the approaches to reduce energy consumption is traffic dependent operation of networks. The traffic demand experienced by the network fluctuates over the duration of a day. Therefore, during the periods of low traffic, we may re-configure the network to trade the excess capacity for energy reduction. For example, we may modulate the BS transmit power (Cell Zooming) so as to maintain the desired QoS. However, determining an optimal network configuration is known to be computationally hard. Along with Cell Zooming, it is essential to also consider channel re-assignment, for, when the transmit powers of BSs are changed, the channels allocated to BSs must also be suitably changed. Considering therefore channel allocations also as state variables, the search space over which the optimization should be performed blows up, further complicating the problem. In this paper, we propose a framework to address this problem. The proposed algorithm is suitable for such large search spaces, while the framework is general enough to admit several QoS requirements and sophisticated power consumption models. The underlying mathematical formulation is also applicable in other contexts, and is of independent interest as well.
Eating Behaviour in the General Population: An Analysis of the Factor Structure of the German Version of the Three-Factor-Eating-Questionnaire (TFEQ) and Its Association with the Body Mass Index

The Three-Factor-Eating-Questionnaire (TFEQ) is an established instrument to assess eating behaviour. Analysis of the TFEQ-factor structure was based on selected, convenient and clinical samples so far. Aims of this study were (I) to analyse the factor structure of the German version of the TFEQ and (II)—based on the refined factor structure—to examine the association between eating behaviour and the body mass index (BMI) in a general population sample of 3,144 middle-aged and older participants (40–79 years) of the ongoing population based cohort study of the Leipzig Research Center for Civilization Diseases (LIFE Health Study). The factor structure was examined in a split-half analysis with both explorative and confirmatory factor analysis. Associations between TFEQ-scores and BMI values were tested with multiple regression analyses controlled for age, gender, and education. We found a three factor solution for the TFEQ with an ‘uncontrolled eating’, a ‘cognitive restraint’ and an ‘emotional eating’ domain including 29 of the original 51 TFEQ-items. Scores of the ‘uncontrolled eating domain’ showed the strongest correlation with BMI values (partial r = 0.26). Subjects with scores above the median in both ‘uncontrolled eating’ and ‘emotional eating’ showed the highest BMI values (mean = 29.41 kg/m²), subjects with scores below the median in all three domains showed the lowest BMI values (mean = 25.68 kg/m²; F = 72.074, p<0.001). Our findings suggest that the TFEQ is suitable to identify subjects with specific patterns of eating behaviour that are associated with higher BMI values. Such information may help health care professionals to develop and implement more tailored interventions for overweight and obese individuals.
TO BE OR NOT TO BE A ZERO PRONOUN : A MACHINE LEARNING APPROACH FOR ROMANIAN

This paper presents a new study on the distribution and identification of zero pronouns in Romanian. A Romanian corpus that includes legal, encyclopaedic, literary, and news texts has been created and manually annotated for zero pronouns. Using a morphological parser for Romanian and machine learning methods, experiments have been performed on the created corpus for the identification of verbs which have a zero pronoun in the subject position. The evaluation results highlight that zero pronouns appear frequently in Romanian, and their distribution depends largely on the genre. Additionally, a search scope for the antecedent has been determined, increasing the chances of correct resolution. Furthermore, more than 70% of the zero pronouns have been accurately identified by various machine learning algorithms. The strong similarity between our results and those obtained for other Romance languages support our conclusions.
Cage-based deformation transfer using mass spring system

classroom use is granted without fee provided that copies are not made or distributed for commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author. SIGGRAPH 2014, August 10 – 14, 2014, Vancouver, British Columbia, Canada. 2014 Copyright held by the Owner/Author. ACM 978-1-4503-2958-3/14/08 Cage-Based Deformation Transfer Using Mass Spring System
Increased ARPP-19 Expression Is Associated with Hepatocellular Carcinoma

The cAMP-regulated phosphoprotein 19 (ARPP-19) plays a key role in cell mitotic G2/M transition. Expression of ARPP-19 was increased in human hepatocellular carcinoma (HCC) compared to adjacent non-tumorous liver tissues in 36 paired liver samples, and the level of ARPP-19 in HCC tissues was positively correlated with the tumor size. To determine the interrelationship between ARPP-19 expression and HCC, we silenced ARPP-19 expression in the human hepatocarcinoma HepG2 and SMMC-7721 cells using lentivirus encoding ARPP-19 siRNA. HepG2 and SMMC-7721 cells with ARPP-19 knockdown displayed lowered cell growth rate, retarded colony formation and increased arrest at the G2/M phase transition. Silencing ARPP-19 in HCC cells resulted in decreased protein levels of phospho-(Ser) CDKs substrates and increased levels of inactivated cyclin division cycle 2 (Cdc2). Therefore, ARPP-19 may play a role in HCC pathogenesis through regulating cell proliferation.
Phonology and the development of the lexicon: evidence from children's errors

ABSTRACT Various kinds of children's lexical errors, mostly based on similarity in sound, are presented and classified. At the earliest stage some children are found to pursue a HOMONYM STRATEGY, actively seeking to combine adult word-patterns to limit their output repertoire. The associations between words underlying these productive homonyms, together with perception-based errors, blends, and other word-substitutions, are compared with malapropisms from a slightly older group of children as well as with data from adults. Analysis of these data makes it possible to chart developmental changes in the phonological links which form one substructure of the lexicon.
Expression of the Bacillus anthracis protective antigen gene by baculovirus and vaccinia virus recombinants

The gene encoding Bacillus anthracis protective antigen (PA) was modified by site-directed mutagenesis, subcloned into baculovirus and vaccinia virus plasmid transfer vectors (pAcYM1 and pSC-11, respectively), and inserted via homologous recombinations into baculovirus Autographa californica nuclear polyhedrosis virus or vaccinia virus (strains WR and Connaught). Expression of PA was detected in both systems by immunofluorescence assays with antisera from rabbits immunized with B. anthracis PA. Western blot (immunoblot) analysis showed that the expressed product of both systems was slightly larger (86 kilodaltons) than B. anthracis-produced PA (83.5 kilodaltons). Analysis of trypsin digests of virus-expressed and authentic PA suggested that the size difference was due to the presence of a signal sequence remaining with the virus-expressed protein. Immunization of mice with either recombinant baculovirus-infected Spodoptera frugiperda cells or with vaccinia virus recombinants elicited a high-titer, anti-PA antibody response.
Upside-down spiders build upside-down orb webs: web asymmetry, spider orientation and running speed in Cyclosa

Almost all spiders building vertical orb webs face downwards when sitting on the hubs of their webs, and their webs exhibit an up–down size asymmetry, with the lower part of the capture area being larger than the upper. However, spiders of the genus Cyclosa, which all build vertical orb webs, exhibit inter- and intraspecific variation in orientation. In particular, Cyclosa ginnaga and C. argenteoalba always face upwards, and C. octotuberculata always face downwards, whereas some C. confusa face upwards and others face downwards or even sideways. These spiders provide a unique opportunity to examine why most spiders face downwards and have asymmetrical webs. We found that upward-facing spiders had upside-down webs with larger upper parts, downward-facing spiders had normal webs with larger lower parts and sideways-facing spiders had more symmetrical webs. Downward-facing C. confusa spiders were larger than upward- and sideways-facing individuals. We also found that during prey attacks, downward-facing spiders ran significantly faster downwards than upwards, which was not the case in upward-facing spiders. These results suggest that the spider's orientation at the hub and web asymmetry enhance its foraging efficiency by minimizing the time to reach prey trapped in the web.
The Local Lyα Forest. I. Observations with the GHRS/G160M on the Hubble Space Telescope

We present the target selection, observations, and data reduction and analysis process for a program aimed at discovering numerous, weak (equivalent width ≤100 mÅ) Lyα absorption lines in the local universe (0.003 ≤ z ≤ 0.069). The purpose of this program is to study the physical conditions of the local intergalactic medium, including absorber distributions in Doppler width and H I column density, redshift evolution of absorber number density, line-of-sight two-point correlation function, and the baryonic content and metallicity. By making use of large-angle, nearby galaxy redshift surveys, we will investigate the relationship (if any) between these Lyα absorbers and galaxies, superclusters, and voids. In Paper I we present high-resolution (∼19 km s-1) spectroscopic observations of 15 very bright (V ≤ 14.5) active galactic nuclei (AGNs) targets made with the Goddard High-Resolution Spectrograph (GHRS) aboard the Hubble Space Telescope (HST). We find 81 definite (≥4 σ) and 30 possible (3-4 σ) Lyα absorption lines in these spectra, which probe a total path length of 116,000 km s-1 (Δz ∼ 0.4) at very low redshift (z ≤ 0.069) and column density (12.5 ≤ log N ≤ 14.5). We found numerous metal lines arising in the Milky Way halo, including absorption from high-velocity clouds in 10 of 15 sight lines and numerous absorptions intrinsic to the target AGN. We present reduced spectra, absorption-line lists, "pie diagrams," showing the known galaxy distributions in the direction of each target, and nearest galaxy tables for each absorber. In Papers II and III, we use the data presented here to determine the basic physical characteristics of the low-z Lyα forest and to investigate the relationship of the absorbers to the local galaxy distribution.
Re-engaging young people through applied learning pedagogy

The Victorian Certificate of Applied Learning (VCAL) was developed as an innovative response to the changing context post-compulsory schooling in Australia. By combining ‘hands-on’ learning approaches with the traditions of adult learning, the VCAL seeks to cater for the learning temperaments and employment pathways of post-compulsory students who are less likely to remain at school to complete a more traditional Victorian Certificate of Education (VCE). This paper draws on my doctoral research into the schooling experience of VCAL students to explore the irony in using adult and work-based learning principles that underpin applied learning pedagogy as a strategy to reengage students frequently considered by schools to be ‘at risk’. It argues that traditional contentdriven and transmissive approaches result in some students being defined ‘at risk’ because of their failure to accept as legitimate traditional school-based modes of learning. It is proposed that teachers in secondary schools require a deeper understanding of applied learning principles and teaching strategies in order to cater for the increasing numbers of applied learning students in the post-compulsory years of secondary schools. It is argued that such an understanding is also critical to avoid many of such students being incorrectly labelled ‘at risk’.
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins

MOTIVATION Transmembrane β barrel proteins (TMBs) are found in the outer membrane of Gram-negative bacteria, chloroplast and mitochondria. They play a major role in the translocation machinery, pore formation, membrane anchoring and ion exchange. TMBs are also promising targets for antimicrobial drugs and vaccines. Given the difficulty in membrane protein structure determination, computational methods to identify TMBs and predict the topology of TMBs are important. RESULTS Here, we present BOCTOPUS; an improved method for the topology prediction of TMBs by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and HMMs account for local and global residue preferences, respectively. Based on a 10-fold cross-validation test, BOCTOPUS performs better than all existing methods, reaching a Q3 accuracy of 87%. Further, BOCTOPUS predicted the correct number of strands for 83% proteins in the dataset. BOCTOPUS might also help in reliable identification of TMBs by using it as an additional filter to methods specialized in this task. AVAILABILITY BOCTOPUS is freely available as a web server at: http://boctopus.cbr. su.se/. The datasets used for training and evaluations are also available from this site.
On the Role of Arbitrageurs in Rational Markets

Price discrepancies, although at odds with mainstream finance, are persistent phenomena in financial markets. These apparent mispricings lead to the presence of ‘arbitrageurs’, who aim to exploit the resulting profit opportunities, but whose role remains controversial. This article investigates the impact of the presence of arbitrageurs in rational financial markets. Arbitrage opportunities between redundant risky assets arise endogenously in an economy populated by rational, heterogeneous investors facing restrictions on leverage and short sales. An arbitrageur, indulging in costless, riskless arbitrage is shown to alleviate the effects of these restrictions and improve the transfer of risk amongst investors. When the arbitrageur lacks market power, they always take on the largest arbitrage position possible. When the arbitrageur behaves noncompetitively, in that they take into account the price impact of their trades, they optimally limit the size of their positions due to decreasing marginal profits. In the case when the arbitrageur is subject to margin requirements and is endowed with capital from outside investors, the size of the arbitrageur’s trades and the capital needed to implement these trades are endogenously solved for in equilibrium.
Aggressive behavior of classical Kaposi's sarcoma and coexistence with angiosarcoma.

UNLABELLED An 82-year-old Caucasian man presented with initially asymptomatic livid red plaques on the plantar surface of the feet that become confluent and evolved into invasively growing nodules accompanied by massive edema. Histology allowed a diagnosis of the classical form of Kaposi's sarcoma; the serology test result for HIV was negative, whereas the associated human herpes virus type 8 was detected by polymerase chain reaction on the skin sample. Over the subsequent 6 months, skin lesions become vegetative and partially necrotic, and extended to the hands and eyelids. Chemotherapy with vinblastine appeared to stabilize the cutaneous disease, but the patient developed a massive gastrointestinal hemorrhage secondary to dissemination to the stomach. Twelve months after the onset of the disease, vegetative and easily bleeding lesions progressively occluded the mouth of the patient: histological features were consistent with a low-grade angiosarcoma distinct from that of Kaposi's sarcoma. The patient could not chew and swallow anymore; he was put on an artificial nutrition but died shortly thereafter. This case illustrates that, even in its classical form, Kaposi's sarcoma may be a malignant, rapidly progressing tumor. LEARNING POINTS a) The extent and rate of spread of initial skin lesions should be considered to be early signs of aggressive dissemination, even in the absence of other variables (i.e., histological pattern, human herpes virus type 8 positive mononuclear cells) associated with progression of the disease. b) An endoscopy may be useful given the high prevalence of gastrointestinal involvement. c) When classical Kaposi's sarcoma displays aggressive behavior a second, primary malignant tumor arising from the vascular tissue should be investigated. TAKE-HOME MESSAGE Even in its classical form, Kaposi's sarcoma may be a malignant, rapidly progressing tumor with visceral involvement; also, a second malignancy may occur in nearly one patient of four. Because localized skin lesions can regress completely with radiotherapy, watchful waiting is probably inappropriate in most cases.
Turning big data into tiny data: Constant-size coresets for k-means, PCA and projective clustering

@d can be approximated up to (1 + e)-factor, for an arbitrary small e > 0, using the O(k/e2)-rank approximation of A and a constant. This implies, for example, that the optimal k-means clustering of the rows of A is (1 + e)-approximated by an optimal k-means clustering of their projection on the O(k/e2) first right singular vectors (principle components) of A. A (j, k)-coreset for projective clustering is a small set of points that yields a (1 + e)-approximation to the sum of squared distances from the n rows of A to any set of k affine subspaces, each of dimension at most j. Our embedding yields (0, k)-coresets of size O(k) for handling k-means queries, (j, 1)-coresets of size O(j) for PCA queries, and (j, k)-coresets of size (log n)O(jk) for any j, k ≥ 1 and constant e e (0, 1/2). Previous coresets usually have a size which is linearly or even exponentially dependent of d, which makes them useless when d ~ n. Using our coresets with the merge-and-reduce approach, we obtain embarrassingly parallel streaming algorithms for problems such as k-means, PCA and projective clustering. These algorithms use update time per point and memory that is polynomial in log n and only linear in d. For cost functions other than squared Euclidean distances we suggest a simple recursive coreset construction that produces coresets of size
Agronomy for sustainable agriculture. A review

Sustainability rests on the principle that we must meet the needs of the present without compromising the ability of future generations to meet their own needs. Starving people in poor nations, obesity in rich nations, increasing food prices, on-going climate changes, increasing fuel and transportation costs, flaws of the global market, worldwide pesticide pollution, pest adaptation and resistance, loss of soil fertility and organic carbon, soil erosion, decreasing biodiversity, desertification, and so on. Despite unprecedented advances in sciences allowing us to visit planets and disclose subatomic particles, serious terrestrial issues about food show clearly that conventional agriculture is no longer suited to feeding humans and preserving ecosystems. Sustainable agriculture is an alternative for solving fundamental and applied issues related to food production in an ecological way (Lal (2008) Agron. Sustain. Dev. 28, 57–64. ). While conventional agriculture is driven almost solely by productivity and profit, sustainable agriculture integrates biological, chemical, physical, ecological, economic and social sciences in a comprehensive way to develop new farming practices that are safe and do not degrade our environment. To address current agronomical issues and to promote worldwide discussions and cooperation we implemented sharp changes at the journal Agronomy for Sustainable Development from 2003 to 2006. Here we report (1) the results of the renovation of the journal and (2) a short overview of current concepts of agronomical research for sustainable agriculture. Considered for a long time as a soft, side science, agronomy is rising fast as a central science because current issues are about food, and humans eat food. This report is the introductory article of the book Sustainable Agriculture, volume 1, published by EDP Sciences and Springer (Lichtfouse et al. (2009) Sustainable Agriculture, Vol. 1, Springer, EDP Sciences, in press).