Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted Genome Modification in Mice Using Zinc-Finger Nucleases

Homologous recombination-based gene targeting using Mus musculus embryonic stem cells has greatly impacted biomedical research. This study presents a powerful new technology for more efficient and less time-consuming gene targeting in mice using embryonic injection of zinc-finger nucleases (ZFNs), which generate site-specific double strand breaks, leading to insertions or deletions via DNA repair by the nonhomologous end joining pathway. Three individual genes, multidrug resistant 1a (Mdr1a), jagged 1 (Jag1), and notch homolog 3 (Notch3), were targeted in FVB/N and C57BL/6 mice. Injection of ZFNs resulted in a range of specific gene deletions, from several nucleotides to >1000 bp in length, among 20–75% of live births. Modified alleles were efficiently transmitted through the germline, and animals homozygous for targeted modifications were obtained in as little as 4 months. In addition, the technology can be adapted to any genetic background, eliminating the need for generations of backcrossing to achieve congenic animals. We also validated the functional disruption of Mdr1a and demonstrated that the ZFN-mediated modifications lead to true knockouts. We conclude that ZFN technology is an efficient and convenient alternative to conventional gene targeting and will greatly facilitate the rapid creation of mouse models and functional genomics research.
Creating 'spaces for diversity' from 'spaces of modernity': The case of the Jane-Finch neighbourhood, Toronto (Canada)

Modernist planning and urban development created a lot of residential space without consulting the people who would live in it. It was generally assumed that the professional planner was the best judge of the needs of the community and knew exactly how to meet these needs through physical design: open green space and high-rise, cheap-to-build apartment blocks with fresh air between them. With these and other principles in mind, modernist planning, produced many neighbourhoods and new towns in an attempt to create 'ideal communities and spaces'. Before long, most of these neighbourhoods and towns had lost their charm and had descended into rundown hubs of poverty, racial and ethnic exclusion, criminality and stigmatisation. Toronto is no stranger to this problem. Jane-Finch, a neighbourhood in the north-western corner of the city is one of the products of modernist planning. JaneFinch, as a cheap neighbourhood, houses a large immigrant population and diverse groups, but thanks to its communityplanning tradition, some social transformations are taking place there and turning a stigmatised rundown area into a community hub. This paper discusses the changing social and spatial dynamics in the Jane-Finch neighbourhood and underlines the need to find new planning approaches in order to deal effectively with an increasingly diverse and complex urban society.
The chains model for detecting parts by their context

Detecting an object part relies on two sources of information - the appearance of the part itself and the context supplied by surrounding parts. In this paper we consider problems in which a target part cannot be recognized reliably using its own appearance, such as detecting low-resolution hands, and must be recognized using the context of surrounding parts. We develop the ‘chains model’ which can locate parts of interest in a robust and precise manner, even when the surrounding context is highly variable and deformable. In the proposed model, the relation between context features and the target part is modeled in a non-parametric manner using an ensemble of feature chains leading from parts in the context to the detection target. The method uses the configuration of the features in the image directly rather than through fitting an articulated 3-D model of the object. In addition, the chains are composable, meaning that new chains observed in the test image can be composed of sub-chains seen during training. Consequently, the model is capable of handling object poses which are infrequent, even non-existent, during training. We test the approach in different settings, including object parts detection, as well as complete object detection. The results show the advantages of the chains model for detecting and localizing parts of complex deformable objects.
Learning to Play Computer Games with Deep Learning and Reinforcement Learning Interim Report

With the integration of deep learning into the traditional ﬁeld of reinforcement learning in the recent decades, the spectrum of applications that artiﬁcial intelligence caters is currently very broad. As using AI to play games is a traditional application of reinforcement learning, the project’s objective is to implement a deep reinforcement learning agent that can defeat a video game. Since it is often diﬃcult to determine which algorithms are appropriate given the wide selection of state-of-the-art techniques in the discipline, proper comparisons and investigations of the algorithms are a prerequisite to implementing such an agent. As a result, this paper serves as a platform for exploring the possibility and eﬀectiveness of using conventional state-of-the-art methods, such as Deep Q Networks and its variants, such as Double Deep Q Networks, are appropriate for game playing, with Deep Q Networks successful in playing a randomized map, further work in this project is needed in order for a comprehensive view of the discipline. Such work in the near future includes the investigation of the use of deep reinforcement learning on games unreported in the literature, or potential improvement to existing deep reinforcement learning techniques. In spite of the technical diﬃculties encountered and minor amendments to the project schedule, the project is still currently on schedule, ie. approximately 50% complete.
Breathers and kinks in a simulated crystal experiment

We develop a simple 1D model for the scattering of an incoming particle hitting the surface of mica crystal, the transmission of energy through the crystal by a localized mode, and the ejection of atom(s) at the incident or distant face. This is the first attempt to model the experiment described in Russell and Eilbeck in 2007 (EPL, 78, 10004). Although very basic, the model shows many interesting features, for example a complicated energy dependent transition between breather modes and a kink mode, and multiple ejections at both incoming and distant surfaces. In addition, the effect of a heavier surface layer is modelled, which can lead to internal reflections of breathers or kinks at the crystal surface.
Spatial Patterns of Whole Brain Grey and White Matter Injury in Patients with Occult Spastic Diplegic Cerebral Palsy

Spastic diplegic cerebral palsy(SDCP)is a common type of cerebral palsy (CP), which presents as a group of motor-impairment syndromes. Previous conventional MRI studies have reported abnormal structural changes in SDCP, such as periventricular leucomalacia. However, there are roughly 27.8% SDCP patients presenting normal appearance in conventional MRI, which were considered as occult SDCP. In this study, sixteen patients with occult SDCP and 16 age- and sex-matched healthy control subjects were collected and the data were acquired on a 3T MR system. We applied voxel-based morphometry (VBM) and tract-based spatial statistics (TBSS) analysis to investigate whole brain grey and white matter injury in occult SDCP. By using VBM method, the grey matter volume reduction was revealed in the bilateral basal ganglia regions, thalamus, insula, and left cerebral peduncle, whereas the white matter atrophy was found to be located in the posterior part of corpus callosum and right posterior corona radiata in the occult SDCP patients. By using TBSS, reduced fractional anisotropy (FA) values were detected in multiple white matter regions, including bilateral white matter tracts in prefrontal lobe, temporal lobe, internal and external capsule, corpus callosum, cingulum, thalamus, brainstem and cerebellum. Additionally, several regions of white matter tracts injury were found to be significantly correlated with motor dysfunction. These results collectively revealed the spatial patterns of whole brain grey and white matter injury in occult SDCP.
Further Evidence That a Placebo Response to Antidepressants Can Be Identified

Objective: The authors ‘ goal was to analyze the acute phase ofantidepressant drug treatment to identify placebo responses. Method: Patients rated as improved after 6 weeks of doubleblind treatment with imipramine or phenelzine were followed for an additional 6 weeks of double-blind treatment. Initial responses were classified according to the speed of improvement (abrupt or gradual), the persistence or nonpersistence of improvement, and the timing ofimprovement (early or late onset). Results: It was predicted that patients with nonpersistent, abrupt responses to the drugs were actually experiencing a placebo response and would have the worst prognosis. In fact, this group accounted for a disproportionate number of the relapses. Nonpersistent responders to a drug had a 23. 7% relapse rate, but persistent responders had only a 9.0% relapse rate, a significant difference. Conclusions: The authors conclude that a significant proportion of relapses within the first 6 weeks of treatment with an active drug are not related to loss of a true drug effect. Rather, some are related to loss of nonspecific placebo effects, and abrupt nonpersistent responses during drug treatment are most likely the result ofplacebo effects. (AmJ Psychiatry 1993; 150:566-570)
Cosmic rays and the magnetic field in the nearby starburst galaxy NGC 253 III. Helical magnetic fields in the nuclear outflow

Context. Magnetic fields are good tracers of gas compression by shock w aves in the interstellar medium. These can be caused by the interaction of star-formation driven outflows from individ ual star formation sites as described in the chimney model. Integration along the line-of-sight and cosmic-ray diffusion may hamper detection of compressed magnetic fields in m any cases. Aims. We study the magnetic field structure in the central part of th e nuclear starburst galaxy NGC 253 with spatial resolutions between 40 and 150 pc to detect any filamentary emission assoc iated with the nuclear outflow. As the nuclear region is much b righter than the rest of the disc we can distinguish this emission fro m that of the disc. Methods. We used radio polarimetric observations with the VLA. New observations at �3 cm with 7. ′′ 5 resolution were combined with archive data at �� 20 and 6 cm. We created a map of the rotation measure distribution between �� 6 and 3 cm and compared it with a synthetic polarization map. Results. We find filamentary radio continuum emission in a geometrical distribution, which we interpret as the boundary of the NW nuclear outflow cone seen in projection. The scaleheight o f the continuum emission is 150± 20 pc, regardless of the observing frequency. The equipartition magnetic field strength is 46 ± 10µG for the total field and 21± 5µG for the regular field in the filaments. We find that the ordered magnetic field is aligned along the fila ments, in agreement with amplification due to compression. T he perpendicular diffusion coeffi cient across the filaments is �⊥ = 1.5× 10 28 cm 2 s −1 · E(GeV) 0.5±0.7 . In the SE part of the nuclear outflow cone the magnetic field is pointing away from the disc in form o f a helix, with an azimuthal component increasing up to at least 1200 pc height, where it is about equal to the total component. The ordered magnetic field in the disc is anisotropic within a radius of 2.2 kpc. At larger radii, the large-scale field is regular and of even parity. Conclusions. The magnetic filaments indicate an interaction of the nuclea r outflow with the interstellar medium. The magnetic field is able to collimate the outflow, which can explain the observ ed small opening angle of≈ 26 ◦ . Owing to the conservation of angular momentum by the plasma in the nuclear outflow, the field lines a re frozen into the plasma, and they wind up into a helix. Strong adiabatic losses of the cosmic-ray electrons in the acceler ated outflow can partly explain why the radio luminosity of th e nucleus lies below the radio-FIR correlation.
Analysis and computation of a least-squares method for consistent mesh tying . 1

In the finite element method, a standard approach to mesh tying is to apply La-grange multipliers. If the interface is curved, however, discretization generally leads to adjoining surfaces that do not coincide spatially. Straightforward Lagrange mul-tiplier methods lead to discrete formulations failing a first-order patch test [18]. This paper presents a theoretical and computational study of a least-squares method for mesh tying [4], applied to the partial differential equation −∇ 2 φ + αφ = f. We prove optimal convergence rates for domains represented as overlapping subdomains and show that the least-squares method passes a patch test of the order of the finite element space by construction. To apply the method to subdomain configurations with gaps and overlaps we use interface perturbations to eliminate the gaps. Theoretical error estimates are illustrated by numerical experiments.
Task constraints and infant grip configurations.

The prehensile grip configurations of infants aged 4 through 8 months were examined as they grasped objects that varied in size and shape. The findings revealed that infants as young as 4 months systematically differentiate grip configurations as a function of the object properties in essentially the same way that 8-month-old infants do. However, the younger 4-month-old infants predominantly used the haptic system in addition to the visual system for information pick-up regarding object properties, whereas 8-month-old infants predominantly used information from the visual system alone to differentiate grip configurations according to the object properties. Infants apparently perceive the same action-relevant information through different emphases of the sensory modes to drive the action system with a similar grip configuration for a given object. It is proposed that the traditional description of an orderly sequence to the development of infant prehension (e.g., Halverson, 1931) is too conservative and inflexible to capture the functionally adaptive prehensile behavior of infants to changing task constraints.
Strategic Alliance Networks and Innovation: A Deterministic and Voluntaristic View Combined

Abstract Over the past decades we have witnessed a tremendous growth in the number of strategic technology alliances and a growing importance of interfirm collaboration in the high-tech sectors. The literature on these topics has grown accordingly. In this respect, our paper serves two aims. One is to provide an overview of the consensus on key issues in this vast body of literature. Second is to identify some major gaps in this literature that may inform future research. In serving these aims, we first discuss the dominant structuralist perspective that stresses the role of embeddedness, but which also reflects a deterministic stance as if firms are subject to an exogenous structure. In contrast, we also explore a more voluntaristic view of how firms may possibly shape their network in view of achieving their strategic aims. This view also seems better able to capture change and network dynamics, an issue that has been largely ignored by the structuralist view.
HiEve: A Corpus for Extracting Event Hierarchies from News Stories

In news stories, event mentions denote real-world events of different spatial and temporal granularity. Narratives in news stories typically describe some real-world event of coarse spatial and temporal granularity along with its subevents. In this work, we present HiEve, a corpus for recognizing relations of spatiotemporal containment between events. In HiEve, the narratives are represented as hierarchies of events based on relations of spatiotemporal containment (i.e., superevent―subevent relations). We describe the process of manual annotation of HiEve. Furthermore, we build a supervised classifier for recognizing spatiotemporal containment between events to serve as a baseline for future research. Preliminary experimental results are encouraging, with classifier performance reaching 58% F1-score, only 11% less than the inter annotator agreement.
Implicit Trust between the Uyghur and the Han in Xinjiang, China

Trust is a vital lubricant that increases the sense of security in social interactions. In this study, we investigated the intergroup trust between the Uyghur and the Han, the two largest ethnic groups in Xinjiang, China, with a Go/No-Go Association Task. Specifically, we instructed Uyghur and Han participants to respond to ethnic faces (Uyghur vs. Han) and trust/distrust words and measured the strength of the automatic associations between the faces and words for both in-group and out-group pairs. As expected, both ethnic groups showed implicit in-group trust and out-group distrust, but the Han group demonstrated stronger in-group trust and out-group distrust toward the Uyghur than the Uyghur group toward the Han. However, the magnitude of distrust of the Han toward the Uyghur was small to medium as compared with that reported by other intergroup relationship research. In addition, participant geographic location was associated with out-group distrust. These findings offer implications for developing effective strategies to encourage trust between conflicting groups.
DEMAPS: A Load-Transition-Based Mobility Management Scheme for an Efficient Selection of MAP in Mobile IPv6 Networks

One major concern for mobile networks consists of finding efficient ways of handling user mobility so that the handover process has minimum effect on users' ongoing sessions. Given the dominance of Internet-based applications in next-generation mobile networks, mobile IP (MIP) has become an important protocol for accommodating the IP mobility. To overcome the excessive delay and signaling involved in the first version of MIP, the hierarchical mobile IPv6 (HMIPv6) protocol has been introduced. The key concept behind HMIPv6 is to locally handle handovers by the usage of an entity called mobility anchor point (MAP). Although the new protocol provides a more efficient way for mobility management in IP networks, it does not control traffic among multiple MAPs in the network. Thus, in many cases, the selected MAP is overloaded, and extensive delays are experienced during the routing process. To tackle this problem, this paper proposes a new technique, i.e., dynamic efficient MAP selection (DEMAPS). The proposed scheme works similar to HMIPv6 when the network is not overloaded. When the network gets heavy loads, the selection of MAPs is based on an estimation of MAP load transition using the exponential moving average method. Simulation results demonstrate that DEMAPS can efficiently balance the signaling traffic load among MAPs and provides a superior network performance compared with traditional HMIP schemes.
Regulation of Bile Acid and Cholesterol Metabolism by PPARs

Bile acids are amphipathic molecules synthesized from cholesterol in the liver. Bile acid synthesis is a major pathway for hepatic cholesterol catabolism. Bile acid synthesis generates bile flow which is important for biliary secretion of free cholesterol, endogenous metabolites, and xenobiotics. Bile acids are biological detergents that facilitate intestinal absorption of lipids and fat-soluble vitamins. Recent studies suggest that bile acids are important metabolic regulators of lipid, glucose, and energy homeostasis. Agonists of peroxisome proliferator-activated receptors (PPARα, PPARγ, PPARδ) regulate lipoprotein metabolism, fatty acid oxidation, glucose homeostasis and inflammation, and therefore are used as anti-diabetic drugs for treatment of dyslipidemia and insulin insistence. Recent studies have shown that activation of PPARα alters bile acid synthesis, conjugation, and transport, and also cholesterol synthesis, absorption and reverse cholesterol transport. This review will focus on the roles of PPARs in the regulation of pathways in bile acid and cholesterol homeostasis, and the therapeutic implications of using PPAR agonists for the treatment of metabolic syndrome.
Macrophage polarization in interstitial lung diseases

The role of bronchoalveolar lavage fluid (BALf) examination in differential diagnosis of interstitial lung diseases (ILD) was established. Currently, functional polarization into M1 (pro-inflammatory) and M2 (anti-inflammatory) subpopulations is emphasized. The aim of our study was to compare the proportion of M1 and M2 in BALf of patients with different ILD. BALf samples were collected from 75 ILD patients: sarcoidosis (SA, 36), hypersensitivity pneumonitis (HP, 10), non-specific interstitial pneumonia (NSIP, 8), idiopathic pulmonary fibrosis (IPF, 6) and other ILD (15). Phenotyping was performed by immunocytochemistry with anti-CD40 and CD163 antibodies (for M1 and M2, respectively). For both, CD40 and CD163, three populations of cells have been specified: small cells with strong (+++), large cells with weak (+) and cells with no (–) reaction. Due to lack of statistically significant differences between patients with HP, NSIP and IPF, they were classified into a common group and compared to the group of patients with sarcoidosis. The median proportion of macrophage population was as follows: for CD40: 61%, 35%, 2% in patients with SA and 49%, 47%, 3% in patients with other ILD and for CD163: 55%, 35%, 5% in SA and 53%, 43%, 1% in ILD patients, respectively. We found a significantly higher proportion of M1 in SA when compared with other ILD. Our study showed no evidence of defined polarization of alveolar macrophages in different types of interstitial lung diseases. However, we emphasized the role of CD40 positive cells in sarcoidosis and the role of CD163 positive cells in fibrotic diffuse lung diseases.
Spatial Orientation Using Map Displays: A Model of the Influence of Target Location

This paper presents a model of human spatial orientation, using a task that involves locating targets on a map of the space. The model uses a hierarchical solution process that was reported by many of the participants in an empirical study. It encodes the location of the target in the visual scene by identifying a cluster of objects that contains the target and then encoding the position of the target within that cluster. By applying this description of the target’s location to the representation on the map of the space, the model is able to correctly identify the target. Using this general strategy, it reproduces all of the major trends in the empirical data.