Miracle-dz/UniFAR-FTUs huggingface dataset:
Measuring rod and cone dynamics in age-related maculopathy.

PURPOSE A cathode-ray-tube (CRT) monitor-based technique was used to isolate clinically significant components of dark adaptation. The utility of the technique in identifying adaptation abnormalities in eyes with age-related maculopathy (ARM) is described. METHODS A CRT dark adaptometer was developed to assess cone and rod recovery after photopigment bleach. The following measures were obtained: cone recovery rate (R(c); in decades per minute) and absolute threshold (Tf(c); log candelas per square meter), rod recovery rate (R(r); decades per minute), and rod-cone transition (rod-cone break [RCB], in minutes). These components were isolated by appropriately selecting stimulus size, stimulus location, pigment bleach, and test duration and by coupling the CRT with judiciously selected neutral-density (ND) filters. The protocol was developed by using 5 young observers and was tested on 27 subjects with ARM in the study eye and 22 age-matched control subjects. RESULTS The parameters necessary for effective isolation of cone and early phase rod dark adaptation were a 2.6 ND filter (for a standard CRT monitor, 0.08-80 cd . m(-2) luminance output); a 4 degrees foveated, 200-ms, achromatic spot; approximately 30% pigment bleaching; and a 30-minute test duration. These settings returned obvious rod and cone recovery curves in control and ARM eyes that were compatible with conventional test methods and identified 93% of participants with ARM as having delayed dynamics in at least one of the parameters. Cone recovery dynamics were significantly slower in the ARM group when compared with age-matched control subjects (R(c), 0.99 +/- 0.35 vs. 2.63 +/- 0.61 decades . min(-1), P < 0.0001). Three of the 27 eyes with ARM did not achieve RCB during the allowed duration (30 minutes). The remaining eyes with ARM (n = 24) exhibited a significant delay in rod recovery (R(r)(,) ARM, 0.16 +/- 0.03 vs. controls, 0.22 +/- 0.02 decades . min(-1), P < 0.0001) and the average time to RCB (+/-SD) in the ARM group was significantly longer than in the control subjects (19.12 +/- 5.17 minutes vs. 10.40 +/- 2.49 minutes, P < 0.0001). CONCLUSIONS The CRT dark-adaptation technique described in this article is an effective test for identifying abnormalities in cone and rod recovery. Slowed cone and rod recovery and a delayed RCB were evident in the eyes with ARM. The test method is potentially useful for clinical intervention trials in which ARM progression is monitored.
Withdrawal of a paper.

A paper entitled “Recombinant human morphogenetic protein-2 for type grade III open segmental tibial fractures from combat injuries in Iraq” was submitted to the JBJS[Br] with a covering letter dated 9 October 2007 which was signed by the authors. The corresponding author was Dr. T. Kukla. The
On the transition to a low latency TCP/IP Internet

Recently, a number of active queue management (AQM) algorithms, such as REM (random exponential marking) and GREEN, have been proposed which reduce the packet queueing backlog and hence reduce the network's latency to close to the propagation delay. This paper uncovers a fundamental problem that a low latency TCP/IP network faces. We call this problem "low latency efficiency collapse". With explicit congestion notification (ECN) still not widely deployed, the main congestion notification remains packet dropping. By reducing the round trip time (RTT) to near the propagation delay, TCP sessions become very aggressive and the packet dropping rate required for congestion notification becomes prohibitively high. A solution to this problem is introduced. It is based on inducing latency. When applied to the new AQMs, it limits the packet loss whilst the Internet makes the transition to ECN. We demonstrate by an experiment that the proposed solution improves the efficiency by about 20%.
Rule-Based Composition Behaviors in Dynamic Plug-In Systems

Plug-in frameworks facilitate the development of customizable and extensible software, yet they often lack support for flexible and dynamic (re)configuration. We have created Plux.NET, a novel plug-in framework for plug-and-play composition. In Plux, a composer replaces programmatic composition with automatic composition. Components just specify their requirements and provisions using metadata, and the composer assembles the components guided by that metadata. This paper introduces rule-based composition behaviors, which are a means for controlling the composition process declaratively. Behavior rules constrain the composer by preventing certain operations or by triggering new ones. They help to establish a rule conformant composition state. Thereby, Plux supports developers in declarative and rule-based composition in order to minimize programming effort.
Stepchild or Prodigy? Neuroprotection in Multiple Sclerosis (MS) Research

Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system (CNS) and characterized by the infiltration of immune cells, demyelination and axonal loss. Loss of axons and nerve fiber pathology are widely accepted as correlates of neurological disability. Hence, it is surprising that the development of neuroprotective therapies has been neglected for a long time. A reason for this could be the diversity of the underlying mechanisms, complex changes in nerve fiber pathology and the absence of biomarkers and tools to quantify neuroregenerative processes. Present therapeutic strategies are aimed at modulating or suppressing the immune response, but do not primarily attenuate axonal pathology. Yet, target-oriented neuroprotective strategies are essential for the treatment of MS, especially as severe damage of nerve fibers mostly occurs in the course of disease progression and cannot be impeded by immune modulatory drugs. This review shall depict the need for neuroprotective strategies and elucidate difficulties and opportunities.
Primary Production of Continental Shelf Waters off New York1

The chlorophyll-radiation method of measuring primary produclion, dcscribcd earlier by the authors, was cmploycd on six oceanographic cruises during 1956-7, each occupying 25 stations across the continental shelf off New York. The relationship pholosynthcsis/ hour (opt. light) :chlorophyll a, using the oxygen production m&hod, was found to agree with that dctermincd earlier from culture and harbor water cxpcriments, dcspitc wide variations of tempcrnturc, nutrients, and the abundance of phytoplankton. The same ratio, with photosynthesis mcasurcd by 04 uptake, was extremely variable and usually lower than that obtained by oxygen-production photosynthesis values. Estimates of daily production bcncalh a square meter of sea surface by the chlorophyllradiation method and in situ Cl4 values agreed within reasonable limits in 75% of the measurements; for the remainder of the times the Cl4 values wcrc consistently lower. Daily production throughout the year ranged roughly from 0.20 to 1.00 g carbon/m2/day within the whole area sludicd. Estimated annual production decreased in a seaward direction from 160 g carbon/m2/ycar in the shallow coastal waters to 100 g carbon/ma/year on the continental HIODC. These values are intermcdiatc bctwccn Riley’s estimates for J,ong Island Sound anci the Sargasso Sea.
Stable Scheduling Policies for Maximizing Throughput in Generalized Constrained Queueing Systems

We consider a class of queueing networks referred to as "generalized constrained queueing networks" which form the basis of several different communication networks and information systems. These networks consist of a collection of queues such that only certain sets of queues can be concurrently served. Whenever a queue is served, the system receives a certain reward. Different rewards are obtained for serving different queues, and furthermore, the reward obtained for serving a queue depends on the set of concurrently served queues. We demonstrate that the dependence of the rewards on the schedules alter fundamental relations between performance metrics like throughput and stability. Specifically, maximizing the throughput is no longer equivalent to maximizing the stability region; we therefore need to maximize one subject to certain constraints on the other. Since stability is critical for bounding packet delays and buffer overflow, we focus on maximizing the throughput subject to stabilizing the system. We design provably optimal scheduling strategies that attain this goal by scheduling the queues for service based on the queue lengths and the rewards provided by different selections. The proposed scheduling strategies are however computationally complex. We subsequently develop techniques to reduce the complexity and yet attain the same throughput and stability region. We demonstrate that our framework is general enough to accommodate random rewards and random scheduling constraints.
Carbon Metabolic Pathways in Phototrophic Bacteria and Their Broader Evolutionary Implications

Photosynthesis is the biological process that converts solar energy to biomass, bio-products, and biofuel. It is the only major natural solar energy storage mechanism on Earth. To satisfy the increased demand for sustainable energy sources and identify the mechanism of photosynthetic carbon assimilation, which is one of the bottlenecks in photosynthesis, it is essential to understand the process of solar energy storage and associated carbon metabolism in photosynthetic organisms. Researchers have employed physiological studies, microbiological chemistry, enzyme assays, genome sequencing, transcriptomics, and 13C-based metabolomics/fluxomics to investigate central carbon metabolism and enzymes that operate in phototrophs. In this report, we review diverse CO2 assimilation pathways, acetate assimilation, carbohydrate catabolism, the tricarboxylic acid cycle and some key, and/or unconventional enzymes in central carbon metabolism of phototrophic microorganisms. We also discuss the reducing equivalent flow during photoautotrophic and photoheterotrophic growth, evolutionary links in the central carbon metabolic network, and correlations between photosynthetic and non-photosynthetic organisms. Considering the metabolic versatility in these fascinating and diverse photosynthetic bacteria, many essential questions in their central carbon metabolism still remain to be addressed.
Designing interaction with molecule visualizations on a multi-touch table

Molecular visualizations are an important tool in modern day biology research. This literature study describes the first step in the process of moving molecule visualizations from desktop computers to multi-touch tables. To control these 2D visualizations of 3D objects on a multi-touch table, a set of gestures has to be defined. Since there is little research about controlling 3D objects on a multi-touch table, several state of the art gestures are examined to see if they are suitable to be used in molecule visualizations. The results show that not every interaction needs to be a multi-touch gesture, and that a user test is needed to confirm if the chosen gesture set is suited for users unfamiliar with multitouch interaction.
Ocular cicatricial pemphigoid review

Purpose of reviewOcular mucous membrane pemphigoid produces progressive cicatrizing conjunctivitis; this can result in scarring of the conjunctiva and cornea. Recent findingsIncreased expression of macrophage-colony-stimulating factor, collagen-binding heat shock protein 47, transforming growth factor-β1, IL-4, IL-5, and macrophage migration inhibitory factor may enhance both conjunctival inflammation and conjunctival scarring. Recent developments on mucous membrane pemphigoid medical therapy include the efficacious effect of daclizumab, intravenous immunoglobulin therapy, and methotrexate. Subconjunctival mitomycin has proved not to be efficacious in controlling long-term, conjunctival inflammation and scarring. The Boston scleral lens enhances vision, reduces the disabling ocular pain and photophobia, and helps to heal persistent epithelial defects, reducing recurrence of defects. Recent developments on mucous membrane pemphigoid surgical therapy include keratolimbal allografts and amniotic membrane transplantation, with or without penetrating keratoplasty for ocular surface reconstruction in total stem cell deficiency. The prognosis is strongly influenced by preoperative conditions such as tear function and functional external ocular adnexae, and by postoperative conditions such as persistent inflammation, severe dry eye, or rejection of the keratolimbal allograft. Some authors find efficacious the use of amniotic membrane transplantation for reconstruction of the conjunctival fornices provided systemic immunosuppression is pre- and post-operatively used. SummaryThe use of daclizumab or intravenous immunoglobulin therapy, the better selection of candidates for surgical interventions, and the better pre- and post-operative management of keratolimbal allograft and amniotic membrane transplantation may improve visual rehabilitation in the patients with ocular mucous membrane pemphigoid.
Approximation with active B-spline curves and surfaces

An active contour model for parametric curve and surface approximation is presented. The active curve or surface adapts to the model shape to be approximated in an optimization algorithm. The quasi-Newton optimization procedure in each iteration step minimizes a quadratic function which is built up with the help of local quadratic approximants of the squared distance function of the model shape and an internal energy which has a smoothing and regularization effect. The approach completely avoids the parametrization problem. We also show how to use a similar strategy for the solution of variational problems for curves on surfaces. Examples are the geodesic path connecting two points on a surface and interpolating or approximating spline curves on surfaces. Finally we indicate how the latter topic leads to the variational design of smooth motions which interpolate or approximate given positions.
A Dynamic Hebbian Learning Algorithm for Constructing E-Learner Communities

In order to solve the problem of "information overflow" in e-learning, an algorithm based on Hebbian learning law is proposed for constructing self-organized communities which can automatically group e-learners according to their learning interests. Unlike filtering methods,this algorithm takes into consideration of the distributed open environment of e-learning. This paper designed a peer-to-peer architecture and applied Hebbian learning law in constructing e-learner communities, avoiding the difficulty in calculating user similarity. Compared with traditional Hebbian learning based algorithm, this algorithm uses dynamic thresholds to address the problem of unilateral trust weight adjustment in extreme cases, and it also improves the trust weight adaptation and neighbor adjustment policies. Experimental results show that this algorithm achieves faster community construction speed and better scalability and stability.
mTOR complex 2 signaling and functions

The mechanistic target of rapamycin (mTOR) plays a central role in cellular growth and metabolism. mTOR forms two distinct protein complexes, mTORC1 and mTORC2. Much is known about the regulation and functions of mTORC1 due to availability of a natural compound, rapamycin, that inhibits this complex. Studies that define mTORC2 cellular functions and signaling have lagged behind. The development of pharmacological inhibitors that block mTOR kinase activity, and thereby inhibit both mTOR complexes, along with availability of mice with genetic knockouts in mTOR complex components have now provided new insights on mTORC2 function and regulation. Since prolonged effects of rapamycin can also disrupt mTORC2, it is worth re-evaluating the contribution of this less-studied mTOR complex in cancer, metabolic disorders and aging. In this review, we focus on recent developments on mammalian mTORC2 signaling mechanisms and its cellular and tissue-specific functions.
Efficient Gene Knock-out and Knock-in with Transgenic Cas9 in Drosophila

Bacterial Cas9 nuclease induces site-specific DNA breaks using small gRNA as guides. Cas9 has been successfully introduced into Drosophila for genome editing. Here, we improve the versatility of this method by developing a transgenic system that expresses Cas9 in the Drosophila germline. Using this system, we induced inheritable knock-out mutations by injecting only the gRNA into embryos, achieved highly efficient mutagenesis by expressing gRNA from the promoter of a novel non-coding RNA gene, and recovered homologous recombination-based knock-in of a fluorescent marker at a rate of 4.5% by co-injecting gRNA with a circular DNA donor.
Deficiency of plasma platelet‐activating factor acetylhydrolase: Roles of blood cells

Platelet‐activating factor (PAF), a potent mediator of inflammation and circulatory shock, is inactivated by the enzyme PAF acetylhydrolase. Plasma PAF acetylhydrolase deficiency occurs even in healthy subjects. We hypothesized that erythrocyte PAF acetylhydrolase could play a supplementary role in this plasma acetylhydrolase deficiency. We examined 1,030 subjects who participated in mass checkups, and assayed plasma and erythrocyte PAF acetylhydrolase. We also investigated the degradation of exogenous PAF by erythrocytes or other blood cells obtained from subjects who exhibited the plasma enzyme deficiency. The incidence of the plasma enzyme deficiency in this general Japanese population was 4.7% (48/1,030). None of the subjects with the deficiency had a history of allergy, circulatory shock, or chronic inflammatory diseases. The mean values for erythrocyte cytosolic PAF acetylhydrolase activity in the normal and deficient subjects were 0.51 ± 0.15 (SD) and 0.71 ± 0.28 nkat (nmol/s)/g protein, respectively, and the difference was significant (P < 0.001, Mann‐Whitney U‐test). The half‐life of 10 nmol/l [3H]PAF in plasma from normal subjects was about 5 min, and the half‐life in whole blood or erythrocyte suspension in autologous plasma was almost the same as that in plasma. In plasma from deficient subjects, unchanged PAF virtually remained and the degradation in whole blood or erythrocyte suspension was a little faster than in plasma. We conclude that erythrocytes contribute only little to PAF metabolism in normal blood but they account for almost all of the slow PAF degradation in blood from subjects deficient in plasma PAF acetylhydrolase. © 1996 Wiley‐Liss, Inc.
Representing Isabelle in LF

LF has been designed and successfully used as a meta-logical framework to represent and reason about object logics. Here we design a representation of the Isabelle logical framework in LF using the recently introduced module system for LF. The major novelty of our approach is that we can naturally represent the advanced Isabelle features of type classes and locales. Our representation of type classes relies on a feature so far lacking in the LF module system: morphism variables and abstraction over them. While conservative over the present system in terms of expressivity, this feature is needed for a representation of type classes that preserves the modular structure. Therefore, we also design the necessary extension of the LF module system.
Nitrous oxide production from soil and manure application: A review

The aim of this review is to summarize the current knowledge about the nitrous oxide (N2 O) production by soils and highlighting future research needs for emission abatement. The article investigates a scientific literature regarding N2 O emissions from the soil according to different factors, such as condition and soil type. Temporal variations can also be explained by the soil temperature and water content. The main review part is focused on solid manure and effluent application to soil. Nitrous oxide gas is formed in soils through the microbiological processes of nitrification and denitrification, and emissions are mainly released after land spreading. Emissions of N2 O are strongly affected by the timing of manure application, reflecting the effects of weather conditions. Key factors for N2 O emissions are the soil moisture, redox potential, available carbon and microbial processes. Recent studies on the effects of seasonal environmental temperature are discussed. Finally, emission factors from land application of solid or effluent manure are listed in table.
Traffic Analysis of UDP-based Flows in Ourmon

We present a custom UDP ﬂow tuple with an IP address key and a set of simple related statistical attributes. At-tributes are used to calculate a per host metric called the UDP work weight which roughly measures the amount of network noise caused by a host. The work weight is used to produce a near real-time sorted top N report for UDP host tuples. We also present a derived attribute based on an algorithm called the UDP guesstimator . The UDP guesstimator roughly classiﬁes port report hosts into various trafﬁc categories including security threats (DOS/scanning) or P2P hosts based on high UDP work weights and other ﬂow attributes. This algorithm does not use Layer 7 data and only relies on Layer 3 and Layer 4 statistics taken from the UDP ﬂow tuple. Although we believe the algorithm to be fairly effective, we discuss several common sources of false positives including DNS servers, and P2P systems which may sometimes appear to be scanners. We also brieﬂy present an exper-iment that has attempted to determine P2P applications based on UDP packet size histogram bins.
Neuropsychological performance in survivors of breast cancer more than 20 years after adjuvant chemotherapy.

PURPOSE Adjuvant chemotherapy for breast cancer can have adverse effects on cognition shortly after administration. Whether chemotherapy has any long-term effects on cognition is largely unknown, yet it becomes increasingly relevant because of the widespread use of chemotherapy for early-stage breast cancer and the improved survival. We investigated whether cyclophosphamide, methotrexate, and fluorouracil (CMF) chemotherapy for breast cancer is associated with worse cognitive performance more than 20 years after treatment. PATIENTS AND METHODS This case-cohort study compared the cognitive performance of patients with breast cancer who had a history of adjuvant CMF chemotherapy treatment (six cycles; average time since treatment, 21 years; n = 196) to that of a population-based sample of women never diagnosed with cancer (n = 1,509). Participants were between 50 and 80 years of age. Exclusion criteria were ever use of adjuvant endocrine therapy, secondary malignancy, recurrence, and/or metastasis. RESULTS The women exposed to chemotherapy performed significantly worse than the reference group on cognitive tests of immediate (P = .015) and delayed verbal memory (P = .002), processing speed (P < .001), executive functioning (P = .013), and psychomotor speed (P = .001). They experienced fewer symptoms of depression (P < .001), yet had significantly more memory complaints on two of three measures that could not be explained by cognitive test performance. CONCLUSION Survivors of breast cancer treated with adjuvant CMF chemotherapy more than 20 years ago perform worse, on average, than random population controls on neuropsychological tests. The pattern of cognitive problems is largely similar to that observed in patients shortly after cessation of chemotherapy. This study suggests that cognitive deficits following breast cancer diagnosis and subsequent CMF chemotherapy can be long lasting.