Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptation of Sindbis Virus to BHK Cells Selects for Use of Heparan Sulfate as an Attachment Receptor

ABSTRACT Attachment of Sindbis virus to the cell surface glycosaminoglycan heparan sulfate (HS) and the selection of this phenotype by cell culture adaptation were investigated. Virus (TR339) was derived from a cDNA clone representing the consensus sequence of strain AR339 (K. L. McKnight, D. A. Simpson, S. C. Lin, T. A. Knott, J. M. Polo, D. F. Pence, D. B. Johannsen, H. W. Heidner, N. L. Davis, and R. E. Johnston, J. Virol. 70:1981–1989, 1996) and from mutant clones containing either one or two dominant cell culture adaptations in the E2 structural glycoprotein (Arg instead of Ser at E2 position 1 [designated TRSB]) or this mutation plus Arg for Ser at E2 114 [designated TRSB-R114]). The consensus virus, TR339, bound to baby hamster kidney (BHK) cells very poorly. The mutation in TRSB increased binding 10- to 50-fold, and the additional mutation in TRSB-R114 increased binding 3- to 5-fold over TRSB. The magnitude of binding was positively correlated with the degree of cell culture adaptation and with attenuation of these viruses in neonatal mice. HS was identified as the attachment receptor for the mutant viruses by the following experimental results. (i) Low concentrations of soluble heparin inhibited plaque formation on and binding of mutant viruses to BHK cells by >95%. In contrast, TR339 showed minimal inhibition at high concentrations. (ii) Binding and infectivity of TRSB-R114 was sensitive to digestion of cell surface HS with heparinase III, and TRSB was sensitive to both heparinase I and heparinase III. TR339 infectivity was only slightly affected by either digestion. (iii) Radiolabeled TRSB and TRSB-R114 attached efficiently to heparin-agarose beads in binding assays, while TR339 showed virtually no binding. (iv) Binding and infectivity of TRSB and TRSB-R114, but not TR339, were greatly reduced on Chinese hamster ovary cells deficient in HS specifically or all glycosaminoglycans. (v) High-multiplicity-of-infection passage of TR339 on BHK cell cultures resulted in rapid coselection of high-affinity binding to BHK cells and attachment to heparin-agarose beads. Sequencing of the passaged virus population revealed a mutation from Glu to Lys at E2 70, a mutation common to many laboratory strains of Sindbis virus. These results suggest that TR339, the most virulent virus tested, attaches to cells through a low-affinity, primarily HS-independent mechanism. Adaptive mutations, selected during cell culture growth of Sindbis virus, enhance binding and infectivity by allowing the virus to attach by an alternative mechanism that is dependent on the presence of cell surface HS.
Application Architecture Discovery - Towards Domain-driven, Easily-Extensible Code Structure

The architecture of a software system and its code structure have a strong impact on its maintainability -- the ability to fix problems, and make changes to the system efficiently. To ensure maintainability, software systems are usually organized as subsystems or modules, each with atomically defined responsibilities. However, as the system evolves, the structure of the system undergoes continuous modifications, drifting away from its original design, leading to functionally non-atomic modules and intertwined dependencies between the modules. In this paper, we propose an approach to improve the code structure and architecture by leveraging the domain knowledge of the system. Our approach exploits the knowledge about the functional architecture of the system to restructure the source code and align physically with the functional elements and the re-usable library layers. The approach is validated by applying to a case study which is an existing financial system. The preliminary analysis for the case-study reveals that the approach creates meaningful structure from the legacy code, which enables the developers to quickly identify the code that implements a given functionality.
Childhood trauma and hallucinations in bipolar affective disorder: preliminary investigation.

BACKGROUND Strong evidence exists for an association between childhood trauma, particularly childhood sexual abuse, and hallucinations in schizophrenia. Hallucinations are also well-documented symptoms in people with bipolar affective disorder. AIMS To investigate the relationship between childhood sexual abuse and other childhood traumas and hallucinations in people with bipolar affective disorder. METHOD A sample of 96 participants was drawn from the Medical Research Council multi-centre trial of cognitive-behavioural therapy for bipolar affective disorder. The trial therapists recorded spontaneous reports of childhood sexual abuse made during the course of therapy. Symptom data were collected by trained research assistants masked to the hypothesis. RESULTS A significant association was found between those reporting general trauma (n=38) and auditory hallucinations. A highly significant association was found between those reporting childhood sexual abuse (n=15) and auditory hallucinations. CONCLUSIONS The relationship between childhood sexual abuse and hallucinations in bipolar disorder warrants further investigation.
Target setting with consideration of target-induced operation variability for performance improvement of semiconductor fabrication

Production target setting is common in practice to guide operations such as machine allocation and lot dispatching to achieve master production schedule (MPS). As targets affect operations and hence wafer flows, wafer flow estimation under given daily production targets is a basis of adjusting targets and machine allocation. This paper presents an innovative design of target setting algorithm (TaSIV) that develops the target-tracking service model by characterizing target-induced mean and variability and designs a hybrid flow time approximation by exploiting transient tendon queue analysis between two stages to set targets for improving production performance. The design first adopts a Bernoulli trial with proportional-to-target probability to model the target-tracking machine allocation and FIFO dispatching and then characterize the target-induced variability (TIV). To capture the effect of TIV on wafer flows, the design then approximates the time for the last wafer in initial WIP of a stage to finish processing at the next stage, named two-stage penetration time approximation, APT-2, by using Markov chain analysis of tandem queues with given initial number of wafers. By Integrating APT-2 into a recursive algorithm, SOPEA, the design estimates penetration time of multiple stages and wafer flows in a fab. Finally, our design integrates APT-2/SOPEA into a fixed-point iteration between wafer flow estimation and capacity allocation for target setting with consideration of TIV. Over a mini-Fab example and given targets generated by TaSIV, simulation of proportional-to-target machine allocation and FIFO dispatching demonstrates that targets generated by TaSIV reduces over-optimism and close to actual moves by 30.7% of bottleneck machine groups as compared to a mean-value based scheme frequently adopted by practitioners of fab operation management. TaSIV also leads to reductions of 1.2% in mean cycle time and 15.4% in cycle time variance at 1.1% throughput increase.
A compreensão e a produção de enunciados metafóricos em crianças com transtornos globais do desenvolvimento

As pesquisas envolvendo a compreensao de enunciados metaforicos por autistas sao unânimes em afirmar que esses individuos nao compreendem metaforas. Os trabalhos que constituem esta tese questionam estas evidencias, com base em teorias contemporâneas nesta area, alem de examinar o potencial valor de um tipo especifico de enunciado metaforico - aproximacoes semânticas- como indicador de diagnostico diferencial entre Transtorno Autista e T. de Asperger. Desta forma, o objetivo do primeiro estudo e apresentar teorias contemporâneas sobre enunciados metaforicos, discutindo-se a hipotese de que a dificuldade dos autistas nao reside exatamente na compreensao de sentidos figurados, mas na sua incapacidade de incluir o contexto e/ou a intencao do outro na interpretacao de um enunciado com sentido figurado. O segundo estudo investigou a relacao entre a) a producao e a compreensao de enunciados metaforicos em criancas com Transtornos Globais do Desenvolvimento e b) enunciados metaforicos, idade de desenvolvimento e a habilidade de Teoria da Mente. Por fim, o terceiro estudo averiguou a qualidade da producao de enunciados metaforicos do tipo aproximacoes semânticas em oito meninos, quatro com Transtorno Autista (AUT) e quatro com Transtorno de Asperger (ASP), equiparados pela idade de desenvolvimento, a fim de se examinar a hipotese levantada em estudos anteriores, de que a ausencia de aproximacoes semânticas por criancas com T. de Asperger poderia ser um indicador precoce desta sindrome. Finalmente, no ultimo capitulo, articulam-se os principais resultados destes tres estudos, avaliando-se criticamente o trabalho realizado e apontando-se rumos para futuras pesquisas. %%%%The research involving metaphorical expressions comprehension by people with autism are unanimous in affirming that these individuals do not understand metaphors. This thesis is composed by different studies that put this evidences into question, based on contemporaneous theories in this field and also examine the potential value of a specific methaforic expression (semantic approximation) as an indicator of differential diagnosis between Autistic Disorder and Asperger´s Disorder. Thus, the aim of the first study is to present contemporaneous theories about metaphorical expressions and to discuss the hypothesis that the difficulty of the autistic persons does not reside exactly in the comprehension of figurative aspects of language, but rather in the incapability of these subjects to take the context and / or the speaker's intention into account when interpretating an utterance with figurative meaning. The second study investigated the relation between a) the production and the comprehension of the metaphorical expressions in children with Pervasive Developmental Disorders and b) metaphorical expressions, developmental age and the Theory of Mind ability. Finally, the third study investigated the quality of the production of metaphorical expressions such as semantic approximations in eight boys, four with Autistic Disorder (AUT) and four with Asperger´s Disorder…
Primal-dual approximation algorithms for a packing-covering pair of problems

We consider a special packing-covering pair of problems. The packing problem is a natural generalization of finding a (weighted) maximum independent set in an interval graph, the covering problem generalizes the problem of finding a (weighted) minimum clique cover in an interval graph. The problem pair involves weights and capacities; we consider the case of unit weights and the case of unit capacities. In each case we describe a simple algorithm that outputs a solution to the packing problem and to the covering problem that are within a factor of 2 of each other. Each of these results implies an approximative min-max result. For the general case of arbitrary weights and capacities we describe an LP-based (2 + e)-approximation algorithm for the covering problem. Finally, we show that, unless P = NP , the covering problem cannot be approximated in polynomial time within arbitrarily good precision.
Identity, Justice and Resistances in the Neoliberal City Session Organizers

As in many other countries, U.S cities have experienced "Neoliberal Urbanization". Originating from 1970s, it, as the reconstitution form of market-guided regulation, has soaked U.S.cities. Since 1980s, and especially 1990s, the process have been associated with dialectical process that is named ”actually existing neoliberalism”, such as conflicted process of the creation and the destruction, and the conflict between or among new and old factions (Brenner & Theodore 2002). As the result, city, the target and experiment lavatory of neoliberal agenda, is called “Neoliberal City”, of which feature is uneven geographical development, especially inner city gentrification. On the other hand, since 1980s, mainly 1990s urban management of many cities has adopted and experienced the new measures and methods, such as PFI and PPP as multi-sectors’ partnership as well as CDC and PDA that seek for neighborhood vitalization. (Paradigm shift in urban management) (Maeyama 2014). This presentation focuses on effectiveness of area management organizations in neoliberal urbanization. Especially through test case of PDAs (Public Development Authority), progressive and unique entities created by city for the mission of area management that have developed themselves mainly in West Coast, we examined the possibilities of intuitional setting for area management as "bulwark" in or against neoliberal urbanization. As the result of our examination on PDAs (such as Pike Place Market PDA ,SCIDpda in Seattle, Washington State), we had the findings: 1) PDA (area management entity that is created and charted by city as special purpose government) emerged in the citizen movement in 1970s. 2 ) Through test study of a typical area management PDA, in terms of demographical analysis ,basically outcome of PDA as key element was perceived that protected the neighborhoods’ character (low income and diverse neighborhood) and activation (keeping the residents) through their comprehensive implementation of projects ,in the neoliberal urbanizing stress. 3) That is related to the advantage (1legal status as public agency (government), 2 institutionally sustained properties. 4)) And we recognized in the essential perspective of related persons to avoid bureaucratization. Indispensable point especially for the potentiality to cope against "capital initiated not citizen grounded -urbanization”.
Anonymous broadcast encryption with an untrusted gateway

We propose a verifiable and anonymous broadcast encryption scheme, where an 'untrusted' gateway can verify incoming communication flows to ensure only the intended anonymous receivers in the target domain can receive them. This scenario is interesting while the privacy of receivers should be considered. The difficulty in this setting is how to achieve both confidentiality of the message and anonymity of receivers during the gateway verification. To achieve this goal, we introduce a new notion of encrypted identity search, which allows the gateway blindly verifies the incoming traffic. Our scheme captures security properties: confidentiality and anonymity against dishonest gateway, corrupted receivers and collusion attacks. We present a concrete construction of gateway-based verifiable and anonymous broadcast encryption system from bilinear pairings, and give its security reduction under the computational assumptions related to bilinear pairings.
Transcribing radio news

We have recently extended the capabilities of BBN's large-vocabulary discrete-utterance speech recognition system (BYBLOS) to operate on raw audio recordings of radio news programming. The recordings are given to the system as large monolithic waveforms without any additional side-information. Our goal is to transcribe all speech in the input with the highest accuracy possible. The problem is very challenging because radio news programming has frequent changes in speaker, speaking style, dialect, accent, topic, channel and environmental conditions. Furthermore, the monolithic input presents new problems for recognition algorithms and language models since all useful boundaries (such as speaker turns or sentence ends) are unknown.
Maternal Methylenetetrahydrofolate Reductase (MTHFR) Homozygosity and Neonatal Outcome: Follow-Up of 42 Pregnancies at Risk

From February 2006 to March 2008, 42 pregnant women homozygous for the 677CT-methylenetetrahydrofolate reductase (MTHFR) allele were recruited in our obstetrics service for pregnancy at risk. All had antithrombotic prophylaxis with low-dose aspirin and/or low-molecular-weight heparin, supplemented with folic acid. In all, 2 women lost the fetus and 4 were lost to follow-up before delivery. A total of 36 women delivered term infants who all underwent transfontanellar ultrasonography within 24 hours of birth. Six (16.6%) had ischemic or hemorrhagic cerebral lesions. No differences were observed in gestational age, birth weight, or umbilical cord pH between the 30 healthy infants and the 6 with cerebral lesions. Neonatal outcomes were negative in spite of maternal folic acid supplementation and antithrombotic prophylaxis during pregnancy. This suggests a relationship between maternal homozygous mutation in the 677CT-MTHFR allele and neonatal cerebral lesions.
A Novel Load Control Strategy For TD-SCDMA Enhanced Uplink

In this paper, we propose a novel load control strategy for TD-SCDMA Enhanced Uplink, called as system-based load control strategy. We compare its performance with the cell-based load control strategy, which was widely accepted in TD-SCDMA release 4/5. It is concluded that system-based load control outperforms cell-based load control in the rise over thermal (RoT) control and the system throughput.
Image retrieval with local and spatial queries

To date most "content-based image retrieval" (CBIR) techniques rely on global attributes such as color or texture histograms which unfortunately ignore the spatial composition of the image. We present an alternative image retrieval system based on the principle that it is the user who is most qualified to specify the query "content" and not the computer. With our system, the user can select multiple "regions-of-interest" and can specify the relevance of their spatial layout in the retrieval process. We also derive similarity bounds on histogram distances for pruning the database search. This experimental system was found to be superior to global indexing techniques as measured by statistical sampling of multiple users' "satisfaction" ratings.
The Relationship between Credit Default Swap Spreads, Bond Yields, and Credit Rating Announcements

A company’s credit default swap spread is the cost per annum for protection against a default by the company. In this paper we analyze data on credit default swap spreads collected by a credit derivatives broker. We first examine the relationship between credit default spreads and bond yields and reach conclusions on the benchmark risk-free rate used by participants in the credit derivatives market. We then carry out a series of tests to explore the extent to which credit rating announcements by Moody’s are anticipated by participants in the credit default swap market.
Multiple murder and the media: A study of the reporting of multiple murder in The Times (1887–1990)

Abstract This study of The Times over a hundred years (1887–1990) identified reports of 2,274 cases of murder of which 237 (or 10 per cent) involved multiple killing. Up until the last decade (1980–90) multiple killing was primarily a familial matter. It further emerged that during the four years 1887–90, around the time of the original Ripper cases, there was an early use of reports from abroad which obscured the reality of multiple killing in England. From the mid-1890s to the mid-1970s the remarkable feature is the paucity of reports of multiple killings in The Times. However, the finding of the incredible rise in reports of multiple killings taking place outside the family context in the most recent decade (1980–90) shows that they are much more widespread than the crimes of child murder and serial killing which have been highlighted by the media. The theoretical puzzle to confront is why the phenomenon of multiple killing has recently expanded in so many guises.
Correlation measurement of squeezed light

We study the implementation of a correlation measurement technique for the characterization of squeezed light which is nearly free of electronic noise. With two different sources of squeezed light, we show that the sign of the covariance coefficient, revealed from the time-resolved correlation data, is witnessing the presence of squeezing in the system. Furthermore, we estimate the degree of squeezing using the correlation method and compare it to the standard homodyne measurement scheme. We show that the role of electronic detector noise is minimized using the correlation approach as opposed to homodyning where it often becomes a crucial issue.
Indocyanine Green Angiography Guided Management of Vogt-Koyanagi-Harada Disease

Purpose To report the management of Vogt-Koyanagi-Harada (VKH) disease based on indocyanine green angiography (ICGA). Methods VKH patients with acute episodes of inflammation (inaugural or recurrent) who had received standard ICGA-guided care were studied retrospectively. Standard of care included high dose systemic corticosteroids at presentation and close ICGA follow-up with addition of immunosuppressive agents and/or intensification of ongoing therapy when recurrent choroidal lesions were detected by ICGA. Visual acuity, number of subclinical recurrences, type and duration of therapy, proportion of quiescent patients after therapy, and ICGA findings were recorded. Results Nine patients including 8 female and one male subject were studied. Five patients had inaugural disease and 4 presented with recurrent acute episodes. Visual acuity increased from 0.86±0.36 to 1.14±0.34 in the right eyes, and from 0.77±0.34 to 1.05±0.33 in the left eyes. The number of ICGA-detected occult choroidal recurrences amounted to 13. Mean duration of treatment was 30.1±34.6 months leading to recurrence-free status after discontinuation of therapy in 6 cases with mean duration of 29.5 months. Conclusion Continuous monitoring and aggressive therapy guided by ICGA in VKH disease prolongs treatment as compared to textbook guidelines but offers the prospect of reaching inflammation-free status after discontinuation of therapy. Zero tolerance to subclinical choroidal inflammation avoids irremediable evolution towards sunset glow fundus in patients treated early after the initial acute inflammatory attack.
The Evolution of School-Based Speech-Language Services

Since their inception nearly 100 years ago, speech-language services in the schools have undergone profound fundamental changes in scope and focus. This article reviews the legislative/ regulatory, societal, professional, and demographic influences that shaped and defined school-based speech-language pathology over the past half century and then describes school-based speech-language practice as it is today. Particular attention is paid to the fundamental elements of contextually based assessments, educationally relevant intervention plans, and increased collaboration/consultation. Finally, strategies are presented that can help to facilitate the changes needed to move from past practice patterns to those that reflect current legislation, research, and practice guidelines.
Instructional Alignment: Searching for a Magic Bullet

When critical features of instructional stimuli match those of assessment, effect sizes routinely reach 1.2 to 3 sigma. An instructional psychologist recasts this classic problem of stimulus control as instructional alignment. This paper describes results of alignment studies that have dramatic Implications for researchers and practitioners. One implication embraces the obvious validity of teaching to the test, but poses what is worth testing as instructional design’s most awesome challenge.
The organization of neocortex in mammals: implications for theories of brain function.

INTRODUCTION 129 TRADITIONAL ARCHITECTONIC THEORIES OF CORTICAL ORGANIZATION 130 DEFINING FIELDS BY M ULTIPLE CRITERIA 132 CURRENT CONCEPTS OF CORTICAL ORGANIZATION 136 Cortical Areas Are Sharply Defined . 136 Cortical Areas Are Functionally Heterogeneous . 137 Species Vary in Number of Areas 139 All Mammals Have Some Fields in Common 139 Major Advances in Brain Evolution Have Been Marked by Increases in Numbers of Unimodal Sensory Areas. 142 Areas Are Multiply Interconnected; Connections Are Species-Variable. 142 Detailed Organization Is Dynamically Maintained. 144 Self-Organization Occurs During Development 145 CONCLUSIONS . 147