Miracle-dz/UniFAR-FTUs huggingface dataset:
Mesenchymal stem cells seeded on a human amniotic membrane improve liver regeneration and mouse survival after extended hepatectomy

Liver failure remains the leading cause of post‐operative mortality after hepatectomy. This study investigated the effect of treatment with allogenic mesenchymal stem cells (MSCs) on survival and liver regeneration 48 hr and 7 days after 80% hepatectomy in C57Bl/6 mice. To optimize their biodistribution, MSCs were grown on acellular human amniotic membranes (HAM) and applied as a patch on the remnant liver. This approach was compared with MSC infusion and HAM patch alone. Hepatectomized mice without any treatment were used as control group. Survival rate was calculated and biological and histopathological parameters were analysed to monitor liver function and regeneration. MSCs grown on HAM retained their ability to proliferate, to differentiate into osteoblasts and adipocytes and to respond to pro‐inflammatory stimuli. Extended hepatectomy (80%) led to liver failure that resulted in death within 72 hr in 76% of mice. MSC infusion showed an early but transitory positive effect on survival. MSC/HAM patches stimulated regeneration and significantly improved survival rate (54% vs. 24% in the control group at 7 days). They also decreased the severity of hepatectomy‐induced steatosis, suggesting a modulation of lipid metabolism in hepatocytes. MSCs were still present on HAM at Days 2 and 7 posthepatectomy. In conclusion, engineered tissue constructs that combine MSCs and HAM improve survival and liver regeneration after 80% hepatectomy in mice. These encouraging results pave the way to potential clinical application.
NIP1;2 is a plasma membrane-localized transporter mediating aluminum uptake, translocation, and tolerance in Arabidopsis

Significance Aluminum (Al) toxicity is a major constraint for crops grown on acid soils. Various plant species have adopted an Al exclusion/avoidance mechanism and/or internal tolerance mechanisms to ameliorate Al toxicity. In Arabidopsis, the root organic acid exudation-based Al exclusion mechanism has been well characterized; however, no evidence for an internal Al tolerance mechanism has been reported. Here we identify NIP1;2 as an Al-malate transporter involved in Al removal from root cell walls and root-to-shoot Al translocation. We report that the NIP1;2-mediated Al-malate transport is dependent on Al-activated root malate efflux mediated by ALMT1 in Arabidopsis. Taken together, our findings demonstrate the importance of the coordination between Al exclusion and internal Al detoxification mechanisms in Al tolerance in Arabidopsis. Members of the aquaporin (AQP) family have been suggested to transport aluminum (Al) in plants; however, the Al form transported by AQPs and the roles of AQPs in Al tolerance remain elusive. Here we report that NIP1;2, a plasma membrane-localized member of the Arabidopsis nodulin 26-like intrinsic protein (NIP) subfamily of the AQP family, facilitates Al-malate transport from the root cell wall into the root symplasm, with subsequent Al xylem loading and root-to-shoot translocation, which are critical steps in an internal Al tolerance mechanism in Arabidopsis. We found that NIP1;2 transcripts are expressed mainly in the root tips, and that this expression is enhanced by Al but not by other metal stresses. Mutations in NIP1;2 lead to hyperaccumulation of toxic Al3+ in the root cell wall, inhibition of root-to-shoot Al translocation, and a significant reduction in Al tolerance. NIP1;2 facilitates the transport of Al-malate, but not Al3+ ions, in both yeast and Arabidopsis. We demonstrate that the formation of the Al-malate complex in the root tip apoplast is a prerequisite for NIP1;2-mediated Al removal from the root cell wall, and that this requires a functional root malate exudation system mediated by the Al-activated malate transporter, ALMT1. Taken together, these findings reveal a critical linkage between the previously identified Al exclusion mechanism based on root malate release and an internal Al tolerance mechanism identified here through the coordinated function of NIP1;2 and ALMT1, which is required for Al removal from the root cell wall, root-to-shoot Al translocation, and overall Al tolerance in Arabidopsis.
Oblivious Data Structures

We design novel, asymptotically more efficient data structures and algorithms for programs whose data access patterns exhibit some degree of predictability. To this end, we propose two novel techniques, a pointer-based technique and a locality-based technique. We show that these two techniques are powerful building blocks in making data structures and algorithms oblivious. Specifically, we apply these techniques to a broad range of commonly used data structures, including maps, sets, priority-queues, stacks, deques; and algorithms, including a memory allocator algorithm, max-flow on graphs with low doubling dimension, and shortest-path distance queries on weighted planar graphs. Our oblivious counterparts of the above outperform the best known ORAM scheme both asymptotically and in practice.
Ghosts in the Machine II: Neural Correlates of Memory Interference from the Previous Trial

Abstract Previous memoranda interfere with working memory. For example, spatial memories are biased toward locations memorized on the previous trial. We predicted, based on attractor network models of memory, that activity in the frontal eye fields (FEFs) encoding a previous target location can persist into the subsequent trial and that this ghost will then bias the readout of the current target. Contrary to this prediction, we find that FEF memory representations appear biased away from (not toward) the previous target location. The behavioral and neural data can be reconciled by a model in which receptive fields of memory neurons converge toward remembered locations, much as receptive fields converge toward attended locations. Convergence increases the resources available to encode the relevant memoranda and decreases overall error in the network, but the residual convergence from the previous trial can give rise to an attractive behavioral bias on the next trial.
rtMEG: A Real-Time Software Interface for Magnetoencephalography

To date, the majority of studies using magnetoencephalography (MEG) rely on off-line analysis of the spatiotemporal properties of brain activity. Real-time MEG feedback could potentially benefit multiple areas of basic and clinical research: brain-machine interfaces, neurofeedback rehabilitation of stroke and spinal cord injury, and new adaptive paradigm designs, among others. We have developed a software interface to stream MEG signals in real time from the 306-channel Elekta Neuromag MEG system to an external workstation. The signals can be accessed with a minimal delay (≤45 ms) when data are sampled at 1000 Hz, which is sufficient for most real-time studies. We also show here that real-time source imaging is possible by demonstrating real-time monitoring and feedback of alpha-band power fluctuations over parieto-occipital and frontal areas. The interface is made available to the academic community as an open-source resource.
Human Herpesvirus 8 Interferon Regulatory Factors 1 and 3 Mediate Replication and Latency Activities via Interactions with USP7 Deubiquitinase

ABSTRACT Human herpesvirus 8 (HHV-8) encodes four viral interferon regulatory factors (vIRF-1 to -4) that likely function to suppress innate immune and cellular stress responses through inhibitory interactions with various cellular proteins involved in these activities. It is notable that vIRF-1 and -4 have been reported to interact with the deubiquitinase ubiquitin-specific protease 7 (USP7), substrates of which include p53 and the p53-targeting and -destabilizing ubiquitin E3 ligase MDM2. Structural studies of vIRF-1 and vIRF-4 USP7 binding sequences in association with USP7 have been reported; both involve interactions with N-terminal-domain residues of USP7 via EGPS and ASTS motifs in vIRF-1 and vIRF-4, respectively, but vIRF-4 residues also contact the catalytic site. However, the biological activities of vIRF-1 and vIRF-4 via USP7 interactions are unknown. Here, we report that vIRF-3, which is latently, as well as lytically, expressed in HHV-8-infected primary effusion lymphoma (PEL) cells, also interacts with USP7—via duplicated EGPS motifs—and that this interaction is important for PEL cell growth and viability. The interaction also contributes to suppression of productive virus replication by vIRF-3, which we identify here. We further show that vIRF-1, which is expressed at low levels in PEL latency, promotes latent PEL cell viability and that this activity and vIRF-1-promoted productive replication (reported previously) involve EGPS motif-mediated USP7 targeting by vIRF-1. This study is the first to identify latent and lytic functions of vIRF-1 and vIRF-3, respectively, and to address the biological activities of these vIRFs through their interactions with USP7. IMPORTANCE HHV-8 is associated with Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease; both latent and lytic viral functions are believed to contribute. Viral interferon regulatory factors specified by HHV-8 are thought to be critically important for successful productive replication through suppression of innate immune and stress responses triggered by the lytic cycle. Latently expressed vIRF-3 contributes significantly to PEL cell survival. Here, we identify ubiquitin-specific protease 7 (USP7) deubiquitinase targeting by vIRF-3 (in addition to previously reported USP7 binding by vIRF-1 and vIRF-4); the importance of vIRF-1 and vIRF-3 interactions with USP7 for latent PEL cell growth and viability; and the positive and negative contributions, respectively, of USP7 targeting by vIRF-1 and vIRF-3 to HHV-8 productive replication. This is the first report of the biological importance of vIRF-1 in PEL cell latency, the modulation of productive replication by vIRF-3, and the contributions of vIRF-USP7 interactions to HHV-8 biology.
Contralateral Bias of High Spatial Frequency Tuning and Cardinal Direction Selectivity in Mouse Visual Cortex

Binocular mechanisms for visual processing are thought to enhance spatial acuity by combining matched input from the two eyes. Studies in the primary visual cortex of carnivores and primates have confirmed that eye-specific neuronal response properties are largely matched. In recent years, the mouse has emerged as a prominent model for binocular visual processing, yet little is known about the spatial frequency tuning of binocular responses in mouse visual cortex. Using calcium imaging in awake mice of both sexes, we show that the spatial frequency preference of cortical responses to the contralateral eye is ∼35% higher than responses to the ipsilateral eye. Furthermore, we find that neurons in binocular visual cortex that respond only to the contralateral eye are tuned to higher spatial frequencies. Binocular neurons that are well matched in spatial frequency preference are also matched in orientation preference. In contrast, we observe that binocularly mismatched cells are more mismatched in orientation tuning. Furthermore, we find that contralateral responses are more direction-selective than ipsilateral responses and are strongly biased to the cardinal directions. The contralateral bias of high spatial frequency tuning was found in both awake and anesthetized recordings. The distinct properties of contralateral cortical responses may reflect the functional segregation of direction-selective, high spatial frequency-preferring neurons in earlier stages of the central visual pathway. Moreover, these results suggest that the development of binocularity and visual acuity may engage distinct circuits in the mouse visual system. SIGNIFICANCE STATEMENT Seeing through two eyes is thought to improve visual acuity by enhancing sensitivity to fine edges. Using calcium imaging of cellular responses in awake mice, we find surprising asymmetries in the spatial processing of eye-specific visual input in binocular primary visual cortex. The contralateral visual pathway is tuned to higher spatial frequencies than the ipsilateral pathway. At the highest spatial frequencies, the contralateral pathway strongly prefers to respond to visual stimuli along the cardinal (horizontal and vertical) axes. These results suggest that monocular, and not binocular, mechanisms set the limit of spatial acuity in mice. Furthermore, they suggest that the development of visual acuity and binocularity in mice involves different circuits.
A User Interaction Bug Analyzer based on Imaging Processing

Context: Mobile applications support a set of user-interaction features that are independent of the application logic. Rotating the device, scrolling, or zooming are examples of such features. Some bugs in mobile applications can be attributed to user-interaction features. Objective: This paper proposes and evaluates a bug analyzer based on userinteraction features that uses digital image processing to find bugs. Method: Our bug analyzer detects bugs by comparing the similarity between images taken before and after a user-interaction. SURF, an interest point detector and descriptor, is used to compare the images. To evaluate the bug analyzer, we conducted a case study with 15 randomly selected mobile applications. First, we identified user-interaction bugs by manually testing the applications. Images were captured before and after applying each user-interaction feature. Then, image pairs were processed with SURF to obtain interest points, from which a similarity percentage was computed, to finally decide whether there was a bug. Results: We performed a total of 49 user-interaction feature tests. When manually testing the applications, 17 bugs were found, whereas when using image processing, 15 bugs were detected. Conclusions: 8 out of 15 mobile applications tested had bugs associated to user-interaction features. Our bug analyzer based on image processing was able to detect 88% (15 out of 17) of the user-interaction bugs found with manual testing. ∗Costa Rica Institute of Technology, Department of Computer Science, Costa Rica.
Resveratrol supplementation reduces pain experience by postmenopausal women

Objective: Pain is a common complaint among postmenopausal women. It has been postulated that vascular dysfunction caused by estrogen decline at menopause plays a key role in the initiation and progression of degradative joint disease, namely age-related osteoarthritis. We evaluated whether supplementation with resveratrol, a phytoestrogen, could improve aspects of well-being such as chronic pain that is commonly experienced by postmenopausal women. Methods: A 14-week randomized, double-blind, placebo-controlled intervention with trans-resveratrol (75 mg, twice daily) was conducted in 80 healthy postmenopausal women. Aspects of well-being, including pain, menopausal symptoms, sleep quality, depressive symptoms, mood states, and quality of life were assessed by Short form-36 at baseline and at the end of treatment. Rating scales were averaged to provide a composite score representing overall well-being. Cerebral vasodilator responsiveness to hypercapnia was also assessed as a surrogate marker for cerebrovascular function. Results: Compared with placebo treatment, there was a significant reduction in pain and an improvement in total well-being after resveratrol supplementation. Both benefits, including measures of quality of life, correlated with improvements in cerebrovascular function. Conclusions: Our preliminary findings indicate potential for resveratrol treatment to reduce chronic pain in age-related osteoarthritis. Resveratrol consumption may also boost perceptions of well-being in postmenopausal women. Further investigation to elucidate underlying mechanisms is warranted.
Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel

One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions.
Delay-Optimal Distributed Resource Allocation for Device-to-Device Communications

In this paper, the resource allocation problem is investigated for Device-to-Device (D2D) communications underlaying cellular networks with bursty traffic arrival. We formulate an infinite horizon average reward constraint Markov decision process (CMDP) that aims at minimizing the average delay under the dropping propability constraint. Then, we present a reduced-state Bellman's equation with linear value function approximation to deal with the curse of dimensionality problem in solving the CMDP. A distributed resource allocation algorithm is derived with low computation complexity and signaling overhead, which consists of a subchannel bidding mechanism to obtain the optimal control action, and a distributed online stochastic learning algorithm to estimate the value function and the optimal Lagrangian Multipliers (LMs). Simulation results show that the performance of our proposed algorithm is very close to that achieved by the offline value iteration algorithm, and is better than various baselines algorithms.
Enhancing Resolution Using Iterative Back-Projection Technique for Image Sequences

A modulated backscatter communication system (e.g., an Electronic Shelf Label (ESL) system) includes a central node (e.g., a ceiling node) and one or more remote nodes (e.g., ESL tags). The central node transmits a downlink radio signal which is reflectively modulated at a remote node to produce a modulated reflected radio signal. At the remote node, a precise-frequency subcarrier signal is modulated with an uplink information signal to produce a modulated signal which is used to produce the modulated reflected radio signal. At the central node, the modulated reflected radio signal is received, detected and narrowband filtered to obtain the modulated subcarrier signal which is then demodulated to obtain the uplink information signal, with great immunity to close to carrier downlink radio noise and fluorescent light backscatter interference.
Direction‐dependent contraction forces on cell boundaries induce collective migration of epithelial cells within their sheet

During early embryonic development, epithelial cells form a monolayer sheet and migrate in a definite direction. This phenomenon, called epithelial cell migration, is an important topic in developmental biology. A characteristic feature of this process is attachment to adjacent cells during migration, which is necessary for maintaining the integrity of the sheet. However, it is unclear how these cohesive cells migrate without breaking their attachments. A mechanism for this phenomenon was recently proposed, in which direction‐dependent contraction forces acting on cell boundaries induce unidirectional epithelial migration. In this review, we examine this proposed mechanism from various aspects and provide theoretical background for the collective migration of epithelial cells. This information may be helpful for investigators to realize the basic principles underlying collective epithelial migration and devise new mechanisms for it.
Fusobacterium necrophorum infection in mice as a model for the study of liver abscess formation and induction of immunity

A mouse model is described in which intraperitoneal injection of Fusobacterium necrophorum results in chronic liver abscesses. Viable bacterial counts from mouse lung, liver, and spleen were obtained after whole organ homogenization. From 2 h to 5 days postchallenge, liver was found to contain more bacteria than lung on a per gram basis. Bacterial counts from liver and spleen were about the same during the first 8 h; thereafter liver was found to contain more bacteria. By day 13, though bacterial counts were equivalent in the three organs, abscesses were only observed in liver. This predilection for the liver may be due to a nutritional and/or microenvironmental factor(s). Blood cultures of infected mice revealed a general lack of bacteremia. Extended immunization with formalin-killed cells was found to protect mice against F. necrophorum infection.
Adolescent and Parent Treatment Goals in an Internet-Delivered Chronic Pain Self-Management Program: Does Agreement of Treatment Goals Matter?

Objective To assess whether adolescent-parent agreement on treatment goals as part of an Internet-delivered cognitive-behavioral pain intervention was associated with adolescent outcomes. 122 adolescent-parent dyads selected two treatment goals. Pain intensity and pain-related disability were assessed at pre-treatment, post-treatment, and 6- and 12-month follow-ups. We compared dyads who had goal agreement versus no agreement. 74 dyads (61%) agreed on one or more treatment goals, most commonly going to school, sports, and sleep. In dyads who chose the same goal, regardless of the content, adolescents had lower pain intensity post-treatment and at follow-up. When goals were categorized by domain, in dyads who agreed on physically active goals, adolescents were more likely to report lower pain intensity compared with other groups. Agreement of goals was not associated with changes in pain-related disability. Agreement on treatment goals may be an important treatment process to maximize outcomes in self-management therapies.
Effects of Parent‐Implemented Early Start Denver Model Intervention on Chinese Toddlers with Autism Spectrum Disorder: A Non‐Randomized Controlled Trial

To evaluate the effects of a 26‐week, high‐intensity, parent‐implemented Early Start Denver Model (P‐ESDM) intervention on developmental outcomes, severity of autism spectrum disorder (ASD), and parental stress of ASD toddlers in China. Subjects in P‐ESDM group (n = 23) were recruited from 1.5‐ to 2.5‐year‐old toddlers who were screened positive in Xuhui and Minhang Districts and were diagnosed with ASD. A community (comparison) group of age‐matched toddlers with ASD (n = 20) was recruited from other areas. Subjects of the P‐ESDM group attended 1.5‐hr parent coaching per week for 26 weeks, and those in the community group received interventions available from communities. Assessments were conducted at baseline (T1) and 26 weeks later (T2). After adjusting for baseline differences between the two groups, P‐ESDM group demonstrated greater improvement than the community group in general development, especially in Language domain. Neither group demonstrated significant change in ASD severity, but the P‐ESDM group showed greater improvement in social affect, parent‐reported social communication and symbolic play than community group did. Finally, parents in P‐ESDM group experienced decreased parenting stress while those in community group showed an opposite trend, though the differences did not reach significant association with the P‐ESDM intervention. Chinese toddlers with ASD receiving 26 weeks of P‐ESDM via regular coaching sessions showed significant greater improvement than those receiving community interventions in multiple aspects of development including social communications. These findings add support to the importance of providing early screening, diagnosis, and immediate referral for evidence‐based interventions to improve outcome of young children with ASD. Autism Res 2018, 11: 654–666. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.