Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling of Retraction and Resection for Intraoperative Updating of Images

OBJECTIVEIntraoperative tissue deformation that occurs during the course of neurosurgical procedures may compromise patient-to-image registration, which is essential for image guidance. A new approach to account for brain shift, using computational methods driven by sparsely available operating room (OR) data, has been augmented with techniques for modeling tissue retraction and resection. METHODSModeling strategies to arbitrarily place and move an intracranial retractor and to excise designated tissue volumes have been implemented within a computationally tractable framework. To illustrate these developments, a surgical case example, which uses OR data and the preoperative neuroanatomic image volume of the patient to generate a highly resolved, heterogeneous, finite-element model, is presented. Surgical procedures involving the retraction of tissue and the resection of a left frontoparietal tumor were simulated computationally, and the simulations were used to update the preoperative image volume to represent the dynamic OR environment. RESULTSRetraction and resection techniques are demonstrated to accurately reflect intraoperative events, thus providing an approach for near-real-time image-updating in the OR. Information regarding subsurface deformation and, in particular, changing tumor margins is presented. Some of the current limitations of the model, with respect to specific tissue mechanical responses, are highlighted. CONCLUSIONThe results presented demonstrate that complex surgical events such as tissue retraction and resection can be incorporated intraoperatively into the model-updating process for brain shift compensation in high-resolution preoperative images.
ATP-Dependent Carboxylation of Acetophenone by a Novel Type of Carboxylase

ABSTRACT Anaerobic ethylbenzene metabolism in the betaproteobacterium Aromatoleum aromaticum is initiated by anaerobic oxidation to acetophenone via (S)-1-phenylethanol. The subsequent carboxylation of acetophenone to benzoylacetate is catalyzed by an acetophenone-induced enzyme, which has been purified and studied. The same enzyme is involved in acetophenone metabolism in the absence of ethylbenzene. Acetophenone carboxylase consists of five subunits with molecular masses of 70, 15, 87, 75, and 34 kDa, whose genes (apcABCDE) form an apparent operon. The enzyme is synthesized at high levels in cells grown on ethylbenzene or acetophenone, but not in cells grown on benzoate. During purification, acetophenone carboxylase dissociates into inactive subcomplexes consisting of the 70-, 15-, 87-, and 75-kDa subunits (apcABCD gene products) and the 34-kDa subunit (apcE gene product), respectively. Acetophenone carboxylase activity was restored by mixing the purified subcomplexes. The enzyme contains 1 Zn2+ ion per αβγδ core complex and is dependent on the presence of Mg2+ or Mn2+. In spite of the presence of Zn in the enzyme, it is strongly inhibited by Zn2+ ions. Carboxylation of acetophenone is dependent on ATP hydrolysis to ADP and Pi, exhibiting a stoichiometry of 2 mol ATP per mol acetophenone carboxylated. The enzyme shows uncoupled ATPase activity with either bicarbonate or acetophenone in the absence of the second substrate. These observations indicate that both substrates may be phosphorylated, which is consistent with isotope exchange activity observed with deuterated acetophenone and inhibition by carbamoylphosphate, a structural analogue of carboxyphosphate. A potential mechanism of ATP-dependent acetophenone carboxylation is suggested.
Buffer unit multiple access (BUMA) protocol: an enhancement to IEEE 802.11b DCF

One of the limitations of IEEE 802.11b DCF protocol is the low bandwidth utilization in the medium-to-high traffic load conditions, and consequently, it achieves low throughput and high mean packet delay. In this paper we propose an extension of the IEEE 802.11b DCF protocol called the buffer unit multiple access (BUMA) protocol that overcomes these shortcoming of the original IEEE 802.11 protocol. The proposed BUMA scheme achieves higher throughput (up to 35%) and lower mean packet delay (up to 87%) than the IEEE 802.11b DCF protocol at medium-to-high traffic load conditions. In this paper the BUMA scheme is described and simulation results are presented to verify the performance
Iterative Hard Thresholding with Near Optimal Projection for Signal Recovery

Recovering signals that have sparse representations under a given dictionary from a set of linear measurements got much attention in the recent decade. However, most of the work has focused on recovering the signal’s representation, forcing the dictionary to be incoherent and with no linear dependencies between small sets of its columns. A series of recent papers show that such dependencies can be allowed by aiming at recovering the signal itself. However, most of these contributions focus on the analysis framework. One exception to these is the work reported in [1], proposing a variant of the CoSaMP for the synthesis model, and showing that signal recovery is possible even in high-coherence cases. In the theoretical study of this technique the existence of an efficient near optimal projection scheme is assumed. In this paper we extend the above work, showing that under very similar assumptions, a variant of IHT can recover the signal in cases where regular IHT fails.
MatchZoo: A Toolkit for Deep Text Matching

In recent years, deep neural models have been widely adopted for text matching tasks, such as question answering and information retrieval, showing improved performance as compared with previous methods. In this paper, we introduce the MatchZoo toolkit that aims to facilitate the designing, comparing and sharing of deep text matching models. Specifically, the toolkit provides a unified data preparation module for different text matching problems, a flexible layer-based model construction process, and a variety of training objectives and evaluation metrics. In addition, the toolkit has implemented two schools of representative deep text matching models, namely representation-focused models and interaction-focused models. Finally, users can easily modify existing models, create and share their own models for text matching in MatchZoo.
Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets

The existing chimera detection programs are not specifically designed for "next generation" sequence data. Technologies like Roche 454 FLX and Titanium have been adapted over the past years especially with the introduction of bacterial tag-encoded FLX/Titanium amplicon pyrosequencing methodologies to produce over one million 250-600 bp 16S rRNA gene reads that need to be depleted of chimeras prior to downstream analysis. Meeting the needs of basic scientists who are venturing into high-throughput microbial diversity studies such as those based upon pyrosequencing and specifically providing a solution for Windows users, the B2C2 software is designed to be able to accept files containing large multi-FASTA formatted sequences and screen for possible chimeras in a high throughput fashion. The graphical user interface (GUI) is also able to batch process multiple files. When compared to popular chimera screening software the B2C2 performed as well or better while dramatically decreasing the amount of time required generating and screening results. Even average computer users are able to interact with the Windows . Net GUI-based application and define the stringency to which the analysis should be done. B2C2 may be downloaded from http://www.researchandtesting. com/B2C2.
Option pricing in the presence of random arbitrage return

We consider option pricing problems when we relax the condition of no arbitrage in the Black–Scholes model. Assuming random noise in the interest rate process, the derived pricing equation is in the form of stochastic partial differential equation. We used Karhunen–Loève expansion to approximate the stochastic term and a combined finite difference/finite element method to effect temporal and “spatial” discretization. Computational examples in which the noise is assumed to be a Ornstein–Uhlenbeck process are provided that illustrate not only the discretization methods used, but the type of results relevant to option pricing that can be obtained from the model.
A high-level DRAM timing, power and area exploration tool

In systems ranging from mobile devices to servers, DRAM has a big impact on performance and contributes a significant part of the total consumed power. The performance and power of the system depends on the architecture of the DRAM chip, the design of the memory controller and the access patterns received by the memory controller. Evaluating the impact of DRAM design decisions therefore requires a holistic approach that includes an appropriate model of the DRAM bank, a realistic controller and DRAM power model, and a representative workload which requires a full system simulator, running a complete software stack. In this paper, we introduce DRAMSpec, an open source high-level DRAM bank modeling tool. As major contribution, we move the DRAM modeling abstraction level from detailed circuit level to the DRAM bank and by the integration in full system simulators we allow system or processor designers (non-DRAM experts) to tune future DRAM architectures for their target applications and use cases. We demonstrate the merits of DRAMSpec by exploring the influence of DRAM row buffer size and the number of banks on performance and power of a server application (memcached). Our new DRAM design offers a 16% DRAM performance improvement and 13% DRAM energy saving compared to standard comodity DDR3 devices. Additionally, we demonstrate how our tool is able to aid in evaluating novel DRAM architectures for which no datasheets are available.
Stability and efficiency of RPL under realistic conditions in Wireless Sensor Networks

The IPv6 Routing Protocol for Low-Power and Lossy Networks (RPL) is one of the emerging routing standards for multihop Wireless Sensor Networks (WSN). RPL is based on the construction of a Destination-Oriented Directed Acyclic Graph (DODAG), which offers a loop-free topology to route data packets. While several routing metrics have been proposed in the literature, it is unclear how they perform with RPL. In this paper, we analyze the impact of different PHY and MAC metrics on the stability and efficiency of RPL. We highlight the fact that realistic conditions lead to instabilities and oscillations in the routing structure. While minimizing the hop length leads to a stable but poor routing structure, more sophisticated link metrics such as ETX reflect more clearly the radio link quality but increase the number of DODAG reconfigurations. We also provided a detailed methodology to measure the DODAG stability and to implement efficiently each routing metric with RPL.
An Improved Exponential Smoothing Model on Rental Trends Prediction of Public Bicycle Stations

We have analyzed the rental trends of public bicycle stations from the real data of PBSS (public bicycle-sharing system) and summarized 3 patterns in the rental trends of public bicycle stations using k-means. The proposed DDIES method in this paper, which has high accuracy in the prediction, is a model based double exponential smoothing model and difference-index smoothing model. The results have shown that our method has higher precision in the prediction of public bicycle.
The processing of facially expressed emotion in persons with self-reported depression and anxiety

The purpose of the present study was to assess whether persons who report significant levels of anxious and depressed symptomatology process facial expressions in a manner different from normal control subjects. Earlier studies tested for putative deficits in the accuracy of qualitative identification of emotion by depressed persons. Procedures were included to investigate the existence of such deficits. Additionally, employing a model which posits that emotions can be represented along two orthogonal dimensions of arousal and pleasantness, procedures were included for assessing whether anxious and depressed persons differ from normal controls in the levels of arousal and pleasantness that they assign to others' facial expressions of different emotions. As hypothesized, although anxious and anxious, depressed subjects ascribed higher levels of arousal to others' facial expressions, they appeared to be no less accurate than normal control subjects in the accuracy with which they categorized facial expressions as representing particular emotions. In contrast to the differences noted in perceived arousal, multidimensional scaling procedures illustrated that all three groups were very similar in terms of the "mental maps" they form of the interrelations between different emotions. Results have interesting implications in that they call into question past findings of qualitative emotion perception
Estrategias y metas en la resolución de conflictos cotidianos entre adolescentes, padres y madres

Resumen Se estudia la gestión de los conflictos familiares según el punto de vista del padre, de la madre y del adolescente en 295 familias biparentales. Se pretende comparar las estrategias y metas que se emplean durante su resolución y analizar el valor predictivo de las metas en la elección de las estrategias. Se seleccionaron seis estrategias y cuatro metas aplicadas a seis situaciones hipotéticas. Se observa un acercamiento activo y racional al conflicto, aunque las madres están más orientadas que los padres y los adolescentes a la negociación y hacer ver su postura, mientras que los adolescentes utilizan más las tácticas impositivas, de manejo de emociones negativas o bien ignoran el conflicto. La tríada presenta una gran coherencia en la estructura de metas y estrategias, más evidente en el padre que en la madre y el adolescente. Aparecen tendencias de edad que indican un declinar del control parental a los 16–17 años, no así del control de los adolescentes, mientras que disminuye a estas edades el uso de estrategias negociadoras por ambas partes.
Evaluation of a Multiplex Assay for Estimation of HIV-1 Incidence

Objectives Accurate methods of estimating HIV-1 incidence are critical for monitoring the status of the epidemic and the impact of prevention strategies. Although several laboratory-based tests have been developed strictly for this purpose, several limitations exist and improved methods or technologies are needed. We sought to further optimize a previously described bead-based, HIV-1-specific multiplex assay with the capability of measuring multiple immune responses for determining recent infection. Methods We refined the customized HIV-1 Bio-Plex assay by determining cutoffs and mean durations of recency (MDR), based on the reactivity to longitudinal seroconversion specimens (n = 1347) from 311 ART-naïve, HIV-1-infected subjects. False-recent rates (FRRs) were calculated for various long-term cohorts, including AIDS patients, individuals on ART, and subtype C specimens. Incidence was estimated for each individual assay analyte from a simulated population with a known incidence of 1%. For improved incidence estimates, multi-analyte algorithms based on combinations of 3 to 6 analytes were evaluated and compared to the performance of each individual analyte. Results The MDR for the six analytes varied from 164.2 to 279.4 days, while the multi-analyte algorithm MDRs were less variable with a minimum and maximum value of 228.4 and 277.9 days, respectively. The FRRs for the 7 multi-analyte algorithms evaluated in this study varied from 0.3% to 3.1%, in a population of ART-naïve, long-term individuals. All algorithms yielded improved incidence estimates as compared to the individual analytes, predicting an incidence of 0.95% to 1.02%. Conclusions The HIV-specific multiplex assay described here measures several distinct immune responses in a single assay, allowing for the consideration of multi-analyte algorithms for improved HIV incidence estimates.
Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain

From faithfulness to spatial memory Natural selection shapes traits to be as adaptive as possible for a given environment. Okhovat et al. show that such varying selection also shapes variation in social behavior and the brain (see the Perspective by Robinson). Variation in male fidelity among monogamous prairie voles reflects differences in the expression, regulation, and epigenetic status of a vasopressin receptor that functions in spatial memory. Thus, the trade-offs males face between fidelity and infidelity may promote heritable variation that is important for spatial memory and maintain variation in their levels of fidelity. Science, this issue p. 1371; see also p. 1310 Trade-offs between fidelity and infidelity in prairie voles can promote heritable differences in the brain. [Also see Perspective by Robinson] Individual variation in social behavior seems ubiquitous, but we know little about how it relates to brain diversity. Among monogamous prairie voles, levels of vasopressin receptor (encoded by the gene avpr1a) in brain regions related to spatial memory predict male space use and sexual fidelity in the field. We find that trade-offs between the benefits of male fidelity and infidelity are reflected in patterns of territorial intrusion, offspring paternity, avpr1a expression, and the evolutionary fitness of alternative avpr1a alleles. DNA variation at the avpr1a locus includes polymorphisms that reliably predict the epigenetic status and neural expression of avpr1a, and patterns of DNA diversity demonstrate that avpr1a regulatory variation has been favored by selection. In prairie voles, trade-offs in the fitness consequences of social behaviors seem to promote neuronal and molecular diversity.
Motive-oriented therapeutic relationship building for patients diagnosed with schizophrenia

Treatment options for patients with schizophrenia demand further improvement. One way to achieve this improvement is the translation of findings from basic research into new specific interventions. Beyond that, addressing the therapy relationship has the potential to enhance both pharmacological and non-pharmacological treatments. This paper introduces motive-oriented therapeutic relationship (MOTR) building for schizophrenia. MOTR enables therapists to proactively adapt to their patient’s needs and to prevent problematic behaviors. For example, a patient might consider medication as helpful in principle, but the rejection of medication might be one of his few remaining means for his acceptable motive to stay autonomous despite hospitalization. A therapist who is motive-oriented proactively offers many degrees of freedom to this patient in order to satisfy his need for autonomy and to weaken the motivational basis for not taking medication. MOTR makes use of findings from basic and psychotherapy research and is generic in this respect, but at the same time guides therapeutic action precisely and flexibly in a patient oriented way.
Assessment for learning and motivation

Assessment is a fundamental driver of what and how students learn. Originally assessment tasks were seen as a straightforward measurement tool; in recent times, however, educators have realised the potential to use this tool in more powerful ways and issues of quality assessment and student motivation have been discussed within current pedagogical theories. When assessment tasks are embedded in the teaching and learning framework, there is a greater chance that students will achieve the intended learning outcomes and be enriched by the experience. A diversity of assessment strategies is used in the teaching of Biology at the University of Western Sydney. These strategies include self reflective and self-evaluative exercises, pre and post quizzes for lectures, writing of dialogue, creating cartoons to explain concepts as well as the more traditional strategies of mid term assessments and summative theory and practical assessments. The aims are to encourage deep understanding and knowledge and develop metacognitive skills. A key feature of these assessment tasks has been their design. The setting of explicit quality criteria, and guidelines for marking and feedback, has involved students and teaching assistants. To evaluate the success of these teaching, learning and assessment strategies, focus groups and surveys of students and teaching assistants were done in 2005 and 2006. Students identified that an important feature of the teaching, learning and assessment strategies was the personal investment by lecturers and teaching assistants.
Investigating factors influencing the adoption of e-learning : Saudi students’ perspective

This research aimed at investigating the factors influencing students‟ intention to adopt e-learning as a supplementary tool (BIS) and for distance education (BID). A model based on the theory of Planned Behaviour (Ajzen, 1985) was developed in which the students‟ attitude (AT), Subjective Norm (SN) and Perceived Behavioural Control (PBC) were proposed as determinants of the students‟ behavioural intention to adopt elearning (BI). The model hypothesised that gender and internet experience moderate the effects of these factors. The model also suggested some factors as antecedents to AT, SN and PBC. The study adopted a mixed methods approach, involving two small-scale qualitative phases and one major quantitative phase. The samples were drawn from students at a Saudi University. The results revealed that the model explained 20% of the students‟ BIS and 41% of the students‟ BID. Moreover, the results revealed that PBC, or the students‟ perceptions of the existence of constraints that can hamper their adoption of e-learning, was the most significant factor influencing their BIS and BID. Furthermore, for the adoption of e-learning to supplement the face-to-face study, SN or the students‟ perceptions of the social pressures put on them to adopt e-learning, was the second important factor influencing their decision, followed by AT. On the other hand, in the context of adopting e-learning for distance education, AT was more significant than the students‟ SN. In addition, gender was found to only moderate the link between PBC and BID. Internet experience was found to moderate the link between AT and BIS as well as the link between PBC and BID. The findings showed that elearning perceived Ease of Use, Usefulness, Interactivity and Flexibility determined AT. The beliefs of the students‟ peers, family and instructors were found to shape their SN. Perceived Accessibility was the most significant antecedent of PBC, followed by Internet Self-Efficacy and finally, University Support. Moreover, the students did not show differences in BIS when they were compared, based on some selected demographics, while they showed differences in BID when they were compared on the same demographics. Semi-structured interviews were also conducted with six students to shed light on some of the results.
Design and Implementation of a TCG-based Integrity Measurement Architecture

We present the design and implementation of a secure integrity measurement system for Linux. All executable content that is loaded onto the Linux system is measured before execution and these measurements are protected by the Trusted Platform Module (TPM) that is part of the Trusted Computing Group (TCG) standards. Our system is the first to extend the TCG trust measurement concepts to dynamic executable content from the BIOS all the way up into the application layer. In effect, we show that many of the Microsoft NGSCB guarantees can be obtained on today's hardware and today's software and that these guarantees do not require a new CPU mode or operating system but merely depend on the availability of an independent trusted entity, a TPM for example. We apply our trust measurement architecture to a web server application where we show how our system can detect undesirable invocations, such as rootkit programs, and that our measurement architecture is practical in terms of the number of measurements taken and the performance impact of making them.