Miracle-dz/UniFAR-FTUs huggingface dataset:
1.55-$\mu$m VCSEL Arrays for High-Bandwidth WDM-PONs

Monolithically integrated long-wavelength vertical-cavity surface-emitting laser arrays of 4, 8, and 12 high-speed devices are presented. These devices have a lithographically defined pitch of 250 μm and feature a per-channel bandwidth of 10 Gb/s over 20 km of standard single-mode fiber. The output performance is very homogenous for the whole array. Emission wavelength is addressable by current-tuning without any bit-error-rate penalty. This allows highly scalable bandwidth for metro-range networks. Through the migration from coarse wavelength-division-multiplexed (WDM) to dense WDM operation, a bandwidth upgrade from 2.5 to 80 Gb/s is feasible without any further investment into the transmitter infrastructure.
Gene sequence data sets analysed using a hierarchical neural clusterer

Evolutionary algorithms have been used to optimise the performance of neural network models before. This paper uses a hybrid approach by permanently attaching a genetic algorithm (GA) to a hierarchical clusterer to investigate appropriate parameter values for producing specific tree-shaped representations for some gene sequence data. It addresses a particular problem where the size of the data set makes the direct use of a GA too time consuming. We show by using a data set nearly two orders of magnitude smaller in the GA investigation that the results can be usefully translated across to the real, much larger data sets. The data sets in question are gene sequences and the aim of the analysis was to cluster short sub-sequences that could represent binding sites that regulate the expression of genes.
Cerebrovascular Accumulation and Increased Blood‐Brain Barrier Permeability to Circulating Alzheimer's Amyloid β Peptide in Aged Squirrel Monkey with Cerebral Amyloid Angiopathy

Abstract: Senescent squirrel monkey is a valuable model to study pathogenesis of cerebrovascular amyloid angiopathy (CAA). Cerebrovascular sequestration and blood‐brain barrier (BBB) permeability to 125I‐amyloid β(1‐40) synthetic peptide (sAβ1‐40) were studied in adult versus aged squirrel monkey 1 h after a single intravenous injection. In aged monkey, the half‐time of elimination of sAβ1‐40, te1/2, was prolonged by 0.6 h, the systemic clearance, ClSS, was reduced from 1.8 to 1.1 ml/min/kg, and the mean residence time of intact peptide in the circulation was increased by 1 h (45%). In adult monkey, cerebrovascular sequestration of intact sAβ1‐40 was significant, and the BBB permeability was 18.6‐fold higher than for inulin. In aged monkey, the sequestration of intact sAβ1‐40 by cortical and leptomeningeal microvessels and the BBB permeability were increased by 5.9, 1.8‐, and 2.1‐fold, respectively, in the presence of an unchanged barrier to inulin. In brain parenchyma of aged animals, 76.1% of circulating sAβ1‐40 remained intact versus 45.7% in adult. We conclude that multiple age‐related systemic effects, i.e., reduced body elimination and systemic clearance of sAβ1‐40, and reduced peripheral metabolism, may act in concert with BBB mechanisms, i.e., increased transendothelial transport and microvascular accumulation of blood‐borne sAβ1‐40, and reduced brain metabolism to enhance the development of CAA.
A distributed engineering database management system for IC design

Describes a distributed engineering database subsystem (DDB) which is an integral part of the framework in the PANDA IC-CAD system. DDB provides a simple but efficient method for organizing the IC design data in a distributed environment. With version management and concurrency control services, DDB supports the iterative, tentative and collaborative nature of the design process. A database schema based on the concept of object and how it is used as the foundation for tool integration are also discussed. <<ETX>>
Invasive Pulmonary Aspergillosis: MRI, CT, and Plain Radiographic Findings and Their Contribution for Early Diagnosis

A prospective study was conducted in 38 patients with nodular lesions on plain chest radiographs and the clinical suspicion of invasive pulmonary aspergillosis (IPA) to assess the diagnostic accuracy of magnetic resonance imaging (MRI) and computed tomography (CT). For early diagnosis of IPA (clinical signs and symptoms 10 days), MRIs showed typical nodular target-like lesions with Gd-DTPA enhancement of the rim area that was not seen in the early course of the disease or in patients with Pseudomonas or staphylococcal infection. In conclusion, MRI findings are not as characteristic as the CT halo sign in diagnosing IPA in the early course of the disease, but the MRI target sign with Gd-DTPA enhancement of the rim area and the “reverse target” on T2-weighted images are strongly suggestive of IPA at a later stage of the disease.
Pathway connectivity and signaling coordination in the yeast stress-activated signaling network

Stressed cells coordinate a multi‐faceted response spanning many levels of physiology. Yet knowledge of the complete stress‐activated regulatory network as well as design principles for signal integration remains incomplete. We developed an experimental and computational approach to integrate available protein interaction data with gene fitness contributions, mutant transcriptome profiles, and phospho‐proteome changes in cells responding to salt stress, to infer the salt‐responsive signaling network in yeast. The inferred subnetwork presented many novel predictions by implicating new regulators, uncovering unrecognized crosstalk between known pathways, and pointing to previously unknown ‘hubs’ of signal integration. We exploited these predictions to show that Cdc14 phosphatase is a central hub in the network and that modification of RNA polymerase II coordinates induction of stress‐defense genes with reduction of growth‐related transcripts. We find that the orthologous human network is enriched for cancer‐causing genes, underscoring the importance of the subnetwork's predictions in understanding stress biology.
Allogeneic Descemet's Membrane Transplantation Enhances Corneal Endothelial Monolayer Formation and Restores Functional Integrity Following Descemet's Stripping.

Purpose To characterize the differences in corneal endothelial wound healing in the presence or absence of Descemet's membrane (DM), in vivo. Methods New-Zealand white rabbits were subjected to 7-mm endothelial wound either by scraping (n = 8; DM intact), peeling (n = 6; DM removed), or a combinatory scrape/peel wound (n = 6). In a second experiment, rabbits underwent peel wound with immediate transplantation of pure decellularized human DM (n = 4). In vivo endothelial migration was assessed via trypan blue staining. Recovery of corneal clarity and thickness was performed by using slit-lamp biomicroscopy and optical coherence tomography. Cell proliferation, phenotype, and morphology were assessed by using immunofluorescence and scanning electron microscopy. Results In vivo wound closure was faster in the presence of DM; 25.4% ± 1.4%/d versus 5.5% ± 0.6%/d (P < 0.0001). At day 8, complete wound closure was seen in all of the scrape samples but none of the peel group, with wound closure preceding clinical recovery by approximately 6 days in the scrape group. Endothelial cells in the scraped areas reformed functional monolayers capable of restoring corneal thickness and transparency whilst those in the peeled area underwent mesenchymal-like transformation resulting in scar formation. Transplanting decellularized DM in animals receiving a peel wound resulted in clarity and thickness comparable to the scrape group. Endothelial proliferation (Ki67 +ve cells) was higher in scraped versus peeled areas: 54.7% ± 3.5% vs. 8.8% ± 0.7%, (P < 0.01). Conclusions The presence of DM promoted endothelial wound healing, proliferation, and maintenance of a normal phenotype. DM transplantation recovered the abnormal peel phenotype back to that observed after endothelial scraping.
Impact of live mulches, cover crops and herbicides on weeds, growth attributes and yield of direct seeded rice (Oryza sativa L.)

A field investigation was conducted during the rainy (Kharif) season of 2014 and 2015 at Varanasi, Uttar Pradesh, to study the impact of live mulches, cover crops and herbicides on weeds, growth attributes and yield in direct seeded rice (Oryza sativa L.). At 30, 60, 90 DAS and harvest, amongst the weed management treatments, Sesbania cover crop fb bispyribac Na 25 g/ha + azimsulfuron 30 g/ha at 15 DAS reduced total weed density and dry weight than sunhemp cover crop fb bispyribac Na 25 g/ha + azimsulfuron 30 g/ha at 15 DAS thus resulting in the lowest weed index except hand weeding at 15 and 35 DAS. At 90 DAS, Sesbania cover crop fb bispyribac Na 25 g/ha + azimsulfuron 30 g/ha at 15 DAS markedly improved plant height, dry matter accumulation, leaf area index, chlorophyll content during both years. Sesbania cover crop fb bispyribac Na 25 g/ha + azimsulfuron 30 g/ha at 15 DAS improved grain and straw yields during both years but higher harvest index in 2014 as compared to sunhemp cover crop fb bispyribac Na 25 g/ha + azimsulfuron 30 g/ha at 15 DAS.
INCORPORATION OF LIPIDS INTO SUBCELLULAR FRACTIONS OF BRAIN OF QUAKING MUTANT

The synthesis of lipids and their assembly into subcellular membrane fractions of the myelin deficient Quaking mutant and control brains was studied in 18‐, 24‐ and 41‐day‐old animals using a double label methodology with14C and 3H acetate as precursors. As a general procedure, Quaking mutants were injected intracranially with 50 μCi [14C]acetate and their littermate controls with 300 μCi [3H]acetate. The animals were killed 3 h post‐injection, their brains were pooled and subcellular fractions prepared from the common homogenate. An 80‐90% decrease in the incorporation of acetate into eleven lipids of myelin in the Quaking mutant was found. This occurred in the face of apparent normal incorporation (relative to microsomes) into lipids of the other main subcellular fractions (nuclear. mitochondrial and synaptosomal) with the exception of decreased incorporation into the myelin‐like fraction at 18 and 24 days. Cholesterol and cerebroside were less readily incorporated into Quaking myelin than the other lipids. Although the microsomal synthesis of cholesterol and cerebroside was depressed by about 30% in the Quaking mutant, the incorporation of cholesterol into nuclear, synaptosomal and mitochondrial fractions was unaffected in the mutant. This indicates that sufficient cholesterol is synthesized for the normal assembly of these organelles. In contrast the incorporation of acetate into cholesterol and cerebroside of Quaking myelin was decreased much more than microsomal synthesis. This latter result is consistent with a defect in the process of myclin membrane assembly
The migration of synthetic magnetic nanoparticle labeled dendritic cells into lymph nodes with optical imaging

Background The successful biotherapy of carcinoma with dendritic cell (DC) vaccines pivotally relies on DCs’ migratory capability into lymph tissues and activation of T cells. Accurate imaging and evaluation of DC migration in vivo have great significance during antitumor treatment with DC vaccine. We herein examined the behavior of DCs influenced by synthetic superparamagnetic iron oxide (SPIO) nanoparticle labeling. Methods γ-Fe2O3 nanoparticles were prepared and DCs, which were induced from bone marrow monocytes of enhanced green fluorescent protein (EGFP) transgenic mice, were labeled. The endocytosis of the SPIO, surface molecules, cell apoptosis and fluorescence intensity of EGFP-DCs were displayed by Prussian blue staining and flow cytometry (FCM), respectively. After EGFP-DCs, labeled with SPIO, were injected into footpads (n = 5) for 24 hours, the mice were examined in vivo by optical imaging (OPI). Meanwhile, confocal imaging and FCM were applied, respectively, to detect the migration of labeled DCs into draining lymph nodes. Results Nearly 100% of cells were labeled by the SPIO, in which the intracellular blue color gradually deepened and the iron contents rose with the increase of labeling iron concentrations. In addition, cell apoptosis and the surface molecules on DCs were at similar levels after SPIO labeling. After confirming that the fluorescence intensity of EGFP on DCs was not influenced by SPIO, the homing ability of EGFP-DCs labeled with SPIO displayed that the fluorescence intensity and the ratios of EGFP-DCs in draining lymph nodes were gradually decreased with the increase of labeling iron concentrations. Conclusion The synthetic SPIO nanoparticles possess perfect labeling ability and biocompatibility. Moreover, DCs labeled with a low dose of SPIO showed stronger migratory capability in vivo.
Improving a Fundamental Measure of Lexical Association

Pointwise mutual information (PMI), a simple measure of lexical association, is part of several algorithms used as models of lexical semantic memory. Typically, it is used as a component of more complex distributional models rather than in isolation. We show that when two simple techniques are applied—(1) down-weighting co-occurrences involving lowfrequency words in order to address PMI’s so-called “frequency bias,” and (2) defining co-occurrences as counts of “events in which instances of word1 and word2 co-occur in a context” rather than “contexts in which word1 and word2 cooccur”—then PMI outperforms default parameterizations of word embedding models in terms of how closely it matches human relatedness judgments. We also identify which downweighting techniques are most helpful. The results suggest that simple measures may be capable of modeling certain phenomena in semantic memory, and that complex models which incorporate PMI might be improved with these modifications.
Clinical and Functional Outcomes following Primary Repair versus Reconstruction of the Medial Patellofemoral Ligament for Recurrent Patellar Instability

Background. The purpose of this study was to compare outcomes of medial patellofemoral ligament (MPFL) repair or reconstruction. Methods. Fourteen knees that underwent MPFL repair and nine (F5, M4) knees that underwent reconstruction at our institution were evaluated for objective and subjective outcomes. The mean age at operation was 20.1 years for repair and 19.8 years for reconstruction. All patients had a minimum of 2 years of follow-up (range: 24–75 months). Patient subjective outcomes were obtained using the International Knee Documentation Committee (IKDC) and Kujala patellofemoral subjective evaluations, as well as Visual Analog (VAS) and Tegner Activity Scales. Bilateral isometric quadriceps strength and vastus medialis obliquus (VMO) and vastus lateralis (VL) surface EMG were measured during maximal isometric quadriceps contractions at 30° and 60° of flexion. Results. There were no redislocations in either group. There was no difference in IKDC (P = 0.16), Kujala (P = 0.43), Tegner (P = 0.12), or VAS (P = 0.05) scores at follow-up. There were no differences between repair and reconstruction in torque generation of the involved side at 30° (P = 0.96) and 60° (P = 0.99). In addition, there was no side to side difference in torque generation or surface EMG activation of VL or VMO. Conclusions. There were minimal differences found between patients undergoing MPFL repair and MPFL reconstruction for the objective and subjective evaluations in this study.
VANETCODE: network coding to enhance cooperative downloading in vehicular ad-hoc networks

Inter-vehicular communication is fast emerging as a popular application for mobile ad-hoc networks. Content distribution in Vehicular Ad-Hoc Networks (VANET) is particularly challenging due to the high mobility, rapidly changing topology and intermittent connectivity observed in these networks. Effective mechanisms are needed to enable rapid sharing of real-time such as traffic warnings and multimedia-rich files. In this paper, we propose a novel network coding based co-operative content distribution scheme called VANETCODE. The randomization introduced by the coding scheme makes distribution efficient. Our scheme also leverages on the broadcast nature of the wireless medium to expedite the dissemination of the encoded blocks amongst the one-hop neighbors and is entirely independent of routing. We have carried out extensive simulations to demonstrate that VANETCODE effectively enhances cooperative content sharing in VANETs without introducing additional overhead.
Bio-inspired algorithms for decentralized round-robin and proportional fair scheduling

In recent years, several models introduced in mathematical biology and natural science have been used as the foundation of networking algorithms. These bio-inspired algorithms often solve complex problems by means of simple and local interactions of individuals. In this work, we consider the development of decentralized scheduling in a small network of self-organizing devices that are modeled as pulse-coupled oscillators (PCOs). By appropriately designing the dynamics of the PCO, the network of devices can converge to a desynchronous state where the nodes naturally separate their transmissions in time. Specifically, by following Peskin's PCO model with inhibitory coupling, we first show that round-robin scheduling can be achieved with weak convergence, where the nodes' transmissions are separated by a constant duration, but the differences of their local clocks continue to shift over time. Then, by having each node accept coupling only from the pulses emitted by a subset of neighboring nodes, we show that it is possible to achieve strict desynchronization, where the difference between local clocks remain fixed over time. More interestingly, by having each node maintain two local clocks, we show that it is possible to further achieve proportional fair scheduling, where the time alloted to each node is proportional to their demands. The convergence of these algorithms is studied both analytically and numerically.
A single amino acid alteration (101L) introduced into murine PrP dramatically alters incubation time of transmissible spongiform encephalopathy

A mutation equivalent to P102L in the human PrP gene, associated with Gerstmann–Straussler syndrome (GSS), has been introduced into the murine PrP gene by gene targeting. Mice homozygous for this mutation (101LL) showed no spontaneous transmissible spongiform encephalopathy (TSE) disease, but had incubation times dramatically different from wild‐type mice following inoculation with different TSE sources. Inoculation with GSS produced disease in 101LL mice in 288 days. Disease was transmitted from these mice to both wild‐type (226 days) and 101LL mice (148 days). In contrast, 101LL mice infected with ME7 had prolonged incubation times (338 days) compared with wild‐type mice (161 days). The 101L mutation does not, therefore, produce any spontaneous genetic disease in mice but significantly alters the incubation time of TSE infection. Additionally, a rapid TSE transmission was demonstrated despite extremely low levels of disease‐associated PrP.
Web-based Education for All: A Tool for Development Adaptive Courseware

: Many Web-based educational applications are expected to be used by very different groups of users without the assistance of a human teacher. Accordingly there is a need for systems which can adapt to users with very different backgrounds, prior knowledge of the subject and learning goals. An electronic textbook is one of the most prominent varieties of Web-based educational systems. In this paper we describe an approach for developing adaptive electronic textbooks and present InterBook - an authoring tool based on this approach which simplifies the development of adaptive electronic textbooks on the Web
Hepatocyte Nuclear Factor 1A Is a Cell-Intrinsic Transcription Factor Required for B Cell Differentiation and Development in Mice

The hepatocyte NF (HNF) family of transcription factors regulates the complex gene networks involved in lipid, carbohydrate, and protein metabolism. In humans, HNF1A mutations cause maturity onset of diabetes in the young type 3, whereas murine HNF6 participates in fetal liver B lymphopoiesis. In this study, we have identified a crucial role for the prototypical member of the family HNF1A in adult bone marrow B lymphopoiesis. HNF1A−/− mice exhibited a clear reduction in total blood and splenic B cells and a further pronounced one in transitional B cells. In HNF1A−/− bone marrow, all B cell progenitors—from pre-pro–/early pro–B cells to immature B cells—were dramatically reduced and their proliferation rate suppressed. IL-7 administration in vivo failed to boost B cell development in HNF1A−/− mice, whereas IL-7 stimulation of HNF1A−/− B cell progenitors in vitro revealed a marked impairment in STAT5 phosphorylation. The B cell differentiation potential of HNF1A−/− common lymphoid progenitors was severely impaired in vitro, and the expression of the B lymphopoiesis-promoting transcription factors E2A, EBF1, Pax5, and Bach2 was reduced in B cell progenitors in vivo. HNF1A−/− bone marrow chimera featured a dramatic defect in B lymphopoiesis recapitulating that of global HNF1A deficiency. The HNF1A−/− lymphopoiesis defect was confined to B cells as T lymphopoiesis was unaffected, and bone marrow common lymphoid progenitors and hematopoietic stem cells were even increased. Our data demonstrate that HNF1A is an important cell-intrinsic transcription factor in adult B lymphopoiesis and suggest the IL-7R/STAT5 module to be causally involved in mediating its function.
Trafficking Networks and the Mexican Drug War∗ (Job Market Paper)

Drug trade-related violence has escalated dramatically in Mexico during the past five years, claiming 40,000 lives and raising concerns about the capacity of the Mexican state to monopolize violence. This study examines how drug traffickers’ economic objectives influence the direct and spillover effects of Mexican policy towards the drug trade. By exploiting variation from close mayoral elections and a network model of drug trafficking, the study develops three sets of results. First, regression discontinuity estimates show that drug trade-related violence in a municipality increases substantially after the close election of a mayor from the conservative National Action Party (PAN), which has spearheaded the war on drug trafficking. This violence consists primarily of individuals involved in the drug trade killing each other. The empirical evidence suggests that the violence reflects rival traffickers’ attempts to wrest control of territories after crackdowns initiated by PAN mayors have challenged the incumbent criminals. Second, the study accurately predicts diversion of drug traffic following close PAN victories. It does this by estimating a model of equilibrium routes for trafficking drugs across the Mexican road network to the U.S. When drug traffic is diverted to other municipalities, drug trade-related violence in these municipalities increases. Moreover, female labor force participation and informal sector wages fall, corroborating qualitative evidence that traffickers extort informal sector producers. Finally, the study uses the trafficking model and estimated spillover effects to examine the allocation of law enforcement resources. Overall, the results demonstrate how traffickers’ economic objectives and constraints imposed by the routes network affect the policy outcomes of the Mexican Drug War.