Miracle-dz/UniFAR-FTUs huggingface dataset:
An N-terminal domain of the Sendai paramyxovirus P protein acts as a chaperone for the NP protein during the nascent chain assembly step of genome replication

Two domains involved in RNA synthesis have recently been found within the N-terminal 77 amino acids of the Sendai virus P protein. One domain is required for RNA synthesis per se and has properties in common with the transactivation domains of cellular transcription factors. The second domain is thought to be specifically required for the nascent chain assembly step in genome replication. We have further mapped this second domain by the construction of chimeric and deleted P proteins to amino acids 33 to 41 of P and by examining the abilities of these P proteins to support DI genome replication in vivo. Using glycerol gradient sedimentation, we have shown that this domain is required to form a stable complex with unassembled NP (P-NP0) and to prevent NP from assembling illegitimately, i.e., independently of the concurrent assembly of a nascent viral genome. Since the P-NP0 complex represents the functional form of unassembled NP which is delivered to the nascent chain during genome replication, and since amino acids 33 to 41 are not required for the stable interaction of P with the assembled NP of the nucleocapsid, this chaperone function of P is not required for mRNA synthesis or the RNA synthesis step of genome replication.
A Believable Group in the Synthetic Mind

In recent years, virtual environments have evolved from single user and single agent, to multi-user and multi-agent. Furthermore, with the emergence of synthetic characters, collaborative virtual environments can now be populated with characters and users, all interacting, collaborating or competing between each other. However, the user’s interaction with the synthetic characters is not always the best, and it is only positive if the characters are able to show a coherent and believable behaviour. Therefore, in scenarios where users and synthetic characters interact as a group, it is very important that the interactions follow a believable group dynamics. Focusing on this problem, we have developed a model that supports the dynamics of a group of synthetic characters, inspired by theories of group dynamics developed in human social psychological sciences. The dynamics is driven by a characterization of the different types of interactions that may occur in the group, which are differentiated in two main categories: the socio-emotional interactions and the task related interactions.
Strategic Incomplete Contracts: Theory and Experiments

We develop a model of strategic contractual incompleteness that identifies conditions under which principals might omit even costlessly verifiable terms. We then use experiments to test comparative statics predictions of the model. While it is well known that verifiability imperfections can limit complete contracting, researchers know less about how the degree of imperfection affects endogenous incompleteness, particularly with repeat trading. In our baseline treatment with perfect verifiability, subjects overwhelmingly used complete contracts to conduct trades, achieving nearly first best outcomes. In our partial verifiability treatment with a reduced set of verifiable performance levels, the results reversed and parties relied heavily on incomplete contracts that omitted even costlessly verifiable terms. However, the efficacy of incomplete contracts in outperforming available complete contracts depends critically on the continuation probability of repeat trading. With a small continuation probability, incomplete contracts did no better than complete contracts while exposing parties to considerable strategic uncertainty.
Pufferfish

In this article, we introduce a new and general privacy framework called Pufferfish. The Pufferfish framework can be used to create new privacy definitions that are customized to the needs of a given application. The goal of Pufferfish is to allow experts in an application domain, who frequently do not have expertise in privacy, to develop rigorous privacy definitions for their data sharing needs. In addition to this, the Pufferfish framework can also be used to study existing privacy definitions. We illustrate the benefits with several applications of this privacy framework: we use it to analyze differential privacy and formalize a connection to attackers who believe that the data records are independent; we use it to create a privacy definition called hedging privacy, which can be used to rule out attackers whose prior beliefs are inconsistent with the data; we use the framework to define and study the notion of composition in a broader context than before; we show how to apply the framework to protect unbounded continuous attributes and aggregate information; and we show how to use the framework to rigorously account for prior data releases.
A theory of case-based decisions

Gilboa and Schmeidler provide a new paradigm for modeling decision making under uncertainty. Case-based decision theory suggests that people make decisions by analogies to past cases: they tend to choose acts that performed well in the past in similar situations, and to avoid acts that performed poorly. The authors describe the general theory and its relationship to planning, repeated choice problems, inductive inference, and learning. They highlight its mathematical and philosophical foundations and compare it to expected utility theory as well as to rule-based systems.
HP1 binding to native chromatin in vitro is determined by the hinge region and not by the chromodomain

We have isolated the complete coding sequences for two Xenopus laevis isoforms of heterochromatin protein 1, corresponding to HP1α and HP1γ. The sequence of xHP1α shows considerable divergence from its mammalian homologues, whereas xHP1γ is highly conserved. Functionally, xHP1α behaves identically to human HP1α. We observe unexpected differences between the two HP1 variants in binding native soluble chromatin, which seem to correlate with their distinct nuclear distributions in vivo. A surprising finding is that the characteristic interaction of HP1 chromodomains with histone H3 at methylated lysine 9 is not detected in preformed chromatin due to its inaccessibility. Instead, we localize a strong chromatin‐binding activity to the short hinge region between the chromodomain and the chromoshadow domain of xHP1α but not xHP1γ. This novel chromatin‐binding activity has a non‐specific DNA‐binding component in addition to a linker histone‐dependent preference for an altered chromatin structure with a likely heterochromatin organization.
Mortality amongst multiple trauma patients admitted to an intensive therapy unit

A retrospective review of 428 severely injured patients admitted to an intensive therapy unit between 1969 and 1982 was performed. The patients' primary injuries were assessed using the injury severity score (ISS), and subsequent complications using the complications impact index and sepsis score. Between 1969 and 1980 mortality fluctuated between 19% and 29% but rose to 47% (p < 0.05) during 1981–82 in spite of an unchanged ISS. The increased mortality was confined to ventilated patients surviving more than 5 days from injury and was associated with multiple organ failure and severe infection. The rapid and sustained increase in mortality could not be explained by any obvious change in severity of injury or referral pattern. The only deliberate change in management related to the combination of analgesic sedative drugs used in ventilated patients. During 1979 to 1982 mortality was 28% in patients given morphine with or without benzodiazepines and 77% in those given morphine and etomidate (p < 0.0005). After discontinuation of the latter regimen (May 1983) and resumption of the former analgesic/sedative combination, mortality fell to 25% (p < 0.005). Possible mechanisms leading to increased mortality include adrenocortical insufficiency or depth of anaesthesia.
Article in Press Evolution and Human Behavior Xxx (2005) Xxx – Xxx

1 2 Applying evolutionary models to the laboratory study 3 of social learning Abstract 14 Cultural evolution is driven, in part, by the strategies that individuals employ to acquire behavior 15 from others. These strategies themselves are partly products of natural selection, making the study of 16 social learning an inherently Darwinian project. Formal models of the evolution of social learning 17 suggest that reliance on social learning should increase with task difficulty and decrease with the 18 probability of environmental change. These models also make predictions about how individuals 19 integrate information from multiple peers. We present the results of microsociety experiments designed 20 to evaluate these predictions. The first experiment measures baseline individual learning strategy in a 21 two-armed bandit environment with variation in task difficulty and temporal fluctuation in the payoffs 22 of the options. Our second experiment addresses how people in the same environment use minimal 23 social information from a single peer. Our third experiment expands on the second by allowing access 24 to the behavior of several other individuals, permitting frequency-dependent strategies like conformity. 25 In each of these experiments, we vary task difficulty and environmental fluctuation. We present several 26 candidate strategies and compute the expected payoffs to each in our experimental environment. We 27 then fit to the data the different models of the use of social information and identify the best-fitting
Pro‐apoptotic therapy with the oligonucleotide GenasenseTM (oblimersen sodium) targeting Bcl‐2 protein expression enhances the biological anti‐tumour activity of rituximab

New strategies have evolved in the treatment of patients with non‐Hodgkin's lymphoma (NHL). Anti‐sense oligonucleotides (ASO) and monoclonal antibody (mAb) therapy, though proven to be safe and effective, have not demonstrated to be curative when used as single agents. We tested an innovative combination strategy involving various mAbs and ASO against Bcl‐2 (G3139) in aggressive preclinical models. G3139, under optimal transfection conditions, decreased the proliferation rate of lymphoma cells by 60–75% when compared with controls. In addition, apoptosis was demonstrated in Raji (25%) and DHL‐4 cells (30%) treated with Genasense following downregulation of Bcl‐2 protein. Downregulation of Bcl‐2 by G3139 was associated with a higher degree of rituximab‐associated, complement‐mediated cytotoxicity and antibody dependent cellular cytotoxicity when compared with rituximab alone‐treated controls. In vivo studies in severe combined immunodeficiency (SCID) mice clearly demonstrated synergistic activity between G3139 and rituximab. Treatment of lymphoma‐bearing SCID mice with G3139 for two consecutive days prior to each rituximab dose resulted in better disease control and survival than treatment with either agent alone or controls. Our findings suggest that Bcl‐2 downregulation by G3139, followed by the administration of rituximab is an efficient anti‐tumour strategy associated with improved survival in lymphoma‐bearing SCID mice.
Recent advances in immunohistochemistry in the diagnosis of ovarian neoplasms

This leader reviews recent advances in immunohistochemistry that are useful in the diagnosis of ovarian neoplasms. These include the value of different anticytokeratin antibodies in the distinction between a primary ovarian adenocarcinoma and a metastatic adenocarcinoma, especially of colorectal origin. These antibodies have also helped to clarify the origin of the peritoneal disease in most cases of pseudomyxoma peritonei. The value of antibodies against so called tumour specific antigens, such as CA125 and HAM56, in determining the ovarian origin of an adenocarcinoma is also reviewed. In recent years, several studies have investigated the value of a variety of monoclonal antibodies in the diagnosis of ovarian sex cord stromal tumours and in the distinction between these neoplasms and their histological mimics. These antibodies include those directed against inhibin, CD99, Mullerian inhibiting substance, relaxin like factor, melan A, and calretinin. Of these, anti-α inhibin appears to be of most diagnostic value. It is stressed that these antibodies should always be used as part of a larger panel and not in isolation.J Clin Pathol(J Clin Pathol 2000;53:327–334)
Long-Term Results of High Tibial Osteotomy for Medial Osteoarthritis of the Knee

Abstract We reviewed retrospectively the results in patients who had undergone one hundred and four high tibial lateral osteotomies. The operations were all performed between 1985 and l993. Each one of fifty men and forty nine women demonstrated a varus deformity of the knee with a coexistent medial osteoarthritis. Results were reviewed in 49 patients (62 knees) with an average follow-up of 10.2 years (range 6-14 years). Of the remaining 42 patients, 8 were lost to follow-up, l0 had died, and 24 were subsequently treated with total knee arthroplasty at an average 4.7 years after having had a high tibial osteotomy. Clinical results were evaluated using the Hospital for Special Surgery Score (HSS) and the Knee Society Score. Radiographs were systematically analysed to evaluate osteoarthritis and leg axis. Forty four (90 per cent) of the forty nine patients stated the results met their expectations and given the same circumstances, they would have the operation once again. In these patients the knee score results were excellent. The same patients had excellent HSS and Knee Society Scores. Five patients (10 per cent) had a poor result and twenty four patients were treated later by total knee arthroplasty because of pain. The following factors set these patients apart from those with more favorable results: previous arthroscopic debridement, obesity, lateral knee osteoarthritis, insufficient valgus correction, and an age of more than 55 years. High tibial valgus osteotomy provides good pain relief and improved function in carefully selected patients. Our results support this conclusion.
Current Management Strategy of Nasopharyngeal Carcinoma

Nasopharyngeal carcinoma is an unique head and neck cancer. It is common among the southern Chinese and is closely associated with the Epstein Barr virus (EBV). To diagnose the disease in its early stage is infrequent as the symptoms are usually trivial and patients only present in late stages. Testing the blood for elevated EBV DNA has now become a screening test for the high risk group of patients, aiming to diagnose the disease in its early stages. Imaging studies, positron emission tomography scans in addition to clinical examination provide information on the extent of the disease. The confirmation of the disease still depends on endoscopic examination and biopsy. Radiotherapy with or without chemotherapy has been the primary treatment modality. The application of intensity modulated radiotherapy and the use of concomitant chemoradiation have improved the control of nasopharyngeal carcinoma together with the reduction of long term side effects. The early detection of residual or recurrence tumor in the neck or at the primary site has allowed delivery of salvage treatment. The choice of the optimal surgical salvage, either for neck disease or primary tumor depends on the extent of the residual or recurrent disease. The outcome of these patients have improved with the application of the appropriate surgical salvage.
Self-Organized Fish Schools: An Examination of Emergent Properties

Heterogeneous, “aggregated” patterns in the spatial distributions of individuals are almost universal across living organisms, from bacteria to higher vertebrates. Whereas specific features of aggregations are often visually striking to human eyes, a heuristic analysis based on human vision is usually not sufficient to answer fundamental questions about how and why organisms aggregate. What are the individual-level behavioral traits that give rise to these features? When qualitatively similar spatial patterns arise from purely physical mechanisms, are these patterns in organisms biologically significant, or are they simply epiphenomena that are likely characteristics of any set of interacting autonomous individuals? If specific features of spatial aggregations do confer advantages or disadvantages in the fitness of group members, how has evolution operated to shape individual behavior in balancing costs and benefits at the individual and group levels? Mathematical models of social behaviors such as schooling in fishes provide a promising avenue to address some of these questions. However, the literature on schooling models has lacked a common framework to objectively and quantitatively characterize relationships between individual-level behaviors and group-level patterns. In this paper, we briefly survey similarities and differences in behavioral algorithms and aggregation statistics among existing schooling models. We present preliminary results of our efforts to develop a modeling framework that synthesizes much of this previous work, and to identify relationships between behavioral parameters and group-level statistics.
Acme: an architecture description interchange language

Numerous architectural description languages (ADLs) have been developed, each providing complementary capabilities for architectural development and analysis. Unfortunately, each ADL and supporting toolset operates in isolation, making it difficult to integrate those tools and share architectural descriptions. Acme is being developed as a joint effort of the software architecture research community as a common interchange format for architecture design tools. Acme provides a structural framework for characterizing architectures, together with annotation facilities for additional ADL-specific information. This scheme permits subsets of ADL tools to share architectural information that is jointly understood, while tolerating the presence of information that falls outside their common vocabulary. In this paper we describe Acme's key features, rationale, and technical innovations.
Acute Disruption of Bone Marrow Hematopoiesis by Benzo(a)pyrene Is Selectively Reversed by Aryl Hydrocarbon Receptor-Mediated Processes

Bone marrow (BM) hematopoietic cells are selectively sensitive to polycyclic aromatic hydrocarbons (PAH) in vivo. 7,12-Dimethylbenz(a)anthracene (DMBA), but not benzo(a)pyrene (BP), depletes BM hematopoietic cells in C57BL/6 mice. This difference is due to a BP-selective aryl hydrocarbon receptor (AhR)-mediated recovery. Colony-forming unit assays show suppression of lymphoid progenitors by each PAH within 6 h but a subsequent recovery, exclusively after BP treatment. Suppression of myeloid progenitors (6 h) occurs only for DMBA. Each progenitor responded equally to DMBA and BP in congenic mice expressing the PAH-resistant AhR (AhRd). AhR, therefore, mediates this BP recovery in each progenitor type. These PAH suppressions depend on Cyp1b1-mediated metabolism. Paradoxically, few genes responded to DMBA, whereas 12 times more responded to BP. Progenitor suppression by DMBA, therefore, occurs with minimal effects on the general BM population. Standard AhR-mediated stimulations (Cyp1a1, Cyp1b1, Ahrr) were similar for each PAH and for the specific agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin but were absent in AhRd mice. A group of 12 such AhR responses was sustained from 6 to 24 h. A second, larger set of BP responses (chemokines, cytokines, cyclooxygenase 2) differed in two respects; DMBA responses were low and BP responses declined extensively from 6 to 24 h. A third cluster exhibited BP-induced increases in protective genes (Nqo1, GST-mu) that appeared only after 12 h. Conversion of BP to quinones contributes oxidative signaling not seen with DMBA. We propose that genes in this second cluster, which share oxidative signaling and AhR activation, provide the AhR-dependent protection of hematopoietic progenitors seen for BP.
Phyllodes Tumor of Breast: A Review Article

Introduction. Phyllodes tumours are rare fibroepithelial lesions. Accurate preoperative pathological diagnosis allows correct surgical planning and avoidance of reoperation. Treatment can be either wide local excision or mastectomy to achieve histologically clear margins. Discussion. The exact aetiology of phyllodes tumour and its relationship with fibroadenoma are unclear. Women aged between 35 and 55 years are commonly involved. The median tumour size is 4 cm but can grow even larger having dilated veins and a blue discoloration over skin. Palpable axillary lymphadenopathy can be identified in up to 10–15% of patients but <1% had pathological positive nodes. Mammography and ultrasonography are main imaging modalities. Cytologically the presence of both epithelial and stromal elements supports the diagnosis. The value of FNAC in diagnosis of phyllodes tumour remains controversial, but core needle biopsy has high sensitivity and negative predictive value. Surgical management is the mainstay and local recurrence in phyllodes tumours has been associated with inadequate local excision. The role of adjuvant radiotherapy and chemotherapy remains uncertain and use of hormonal therapy has not been fully investigated. Conclusion. The preoperative diagnosis and proper management are crucial in phyllodes tumours because of their tendency to recur and malignant potential in some of these tumours.
Lower Newborn Bone Mineral Content Associated With Maternal Use of Tenofovir Disoproxil Fumarate During Pregnancy.

BACKGROUND Fetal bone effects of maternal tenofovir use have not been well studied. We sought to compare whole-body bone mineral content (BMC) of newborns exposed vs not exposed to tenofovir in utero. METHODS We enrolled participants from April 2011 to June 2013 at 14 US clinical sites. Singleton infants of women with human immunodeficiency virus (HIV) infection who took tenofovir in late pregnancy (tenofovir-exposed) or no tenofovir during pregnancy (tenofovir-unexposed) were enrolled during late pregnancy or within 72 hours of birth. Infants born before 36 weeks gestation or with confirmed HIV infection were excluded. Whole-body BMC was measured in the first month of life and compared with that of the tenofovir-exposed and tenofovir-unexposed newborns, unadjusted and adjusted for covariates. RESULTS Seventy-four tenofovir-exposed and 69 tenofovir-unexposed infants had evaluable BMC measurements. Tenofovir-exposed mothers were more likely to be married (31% vs 22%; P = .04) and to use boosted protease inhibitors (84% vs 62%; P = .004). Tenofovir-exposed newborns did not differ from unexposed newborns on mean gestational age (38.2 vs 38.1 weeks) or mean length (-0.41 vs -0.18) or weight (-0.71 vs -0.48) Z-scores. The mean (standard deviation) BMC of tenofovir-exposed infants was 12% lower than for unexposed infants (56.0 [11.8] vs 63.8 [16.6] g; P = .002). The adjusted mean bone mineral content was 5.3 g lower (95% confidence interval, -9.5, -1.2; P = .013) in the tenofovir-exposed infants. CONCLUSIONS Maternal tenofovir use is associated with significantly lower neonatal BMC. The duration and clinical significance of this finding should be evaluated in longitudinal studies. CLINICAL TRIALS REGISTRATION ClinicalTrials.gov NCT01310023.