Miracle-dz/UniFAR-FTUs huggingface dataset:
Continuous program optimization: A case study

Much of the software in everyday operation is not making optimal use of the hardware on which it actually runs. Among the reasons for this discrepancy are hardware/software mismatches, modularization overheads introduced by software engineering considerations, and the inability of systems to adapt to users' behaviors.A solution to these problems is to delay code generation until load time. This is the earliest point at which a piece of software can be fine-tuned to the actual capabilities of the hardware on which it is about to be executed, and also the earliest point at wich modularization overheads can be overcome by global optimization.A still better match between software and hardware can be achieved by replacing the already executing software at regular intervals by new versions constructed on-the-fly using a background code re-optimizer. This not only enables the use of live profiling data to guide optimization decisions, but also facilitates adaptation to changing usage patterns and the late addition of dynamic link libraries.This paper presents a system that provides code generation at load-time and continuous program optimization at run-time. First, the architecture of the system is presented. Then, two optimization techniques are discussed that were developed specifically in the context of continuous optimization. The first of these optimizations continually adjusts the storage layouts of dynamic data structures to maximize data cache locality, while the second performs profile-driven instruction re-scheduling to increase instruction-level parallelism. These two optimizations have very different cost/benefit ratios, presented in a series of benchmarks. The paper concludes with an outlook to future research directions and an enumeration of some remaining research problems.The empirical results presented in this paper make a case in favor of continuous optimization, but indicate that it needs to be applied judiciously. In many situations, the costs of dynamic optimizations outweigh their benefit, so that no break-even point is ever reached. In favorable circumstances, on the other hand, speed-ups of over 120% have been observed. It appears as if the main beneficiaries of continuous optimization are shared libraries, which at different times can be optimized in the context of the currently dominant client application.
On levels of detail in terrains

In many applications it is important that one can view a scene at di erent levels of detail. A prime example is ight simulation: a high level of detail is needed when ying low, whereas a low level of detail su ces when ying high. More precisely, one would like to visualize the part of the scene that is close at a high level of detail, and the part that is far away at a low level of detail. We propose a hierarchy of detail levels for a polyhedral terrain (or, triangulated irregular network) that allows this: given a view point, it is possible to select the appropriate level of detail for each part of the terrain in such a way that the parts still t together continuously. The main advantage of our structure is that it uses the Delaunay triangulation at each level, so that triangles with very small angles are avoided. This is the rst method that uses the Delaunay triangulation and still allows to combine di erent levels into a single representation.
Expression of cone-photoreceptor-specific antigens in a cell line derived from retinal tumors in transgenic mice.

PURPOSE To examine an immortalized mouse retinal cell line (661W) for markers characteristic of photoreceptor cells and validate its photoreceptor origin. METHODS The 661W cells were cloned from retinal tumors of a transgenic mouse line that expresses the simian virus (SV) 40 T antigen under control of the human interphotoreceptor retinol-binding protein (IRBP) promoter. Morphologic, immunocytochemical, and immunoblot analyses were performed to characterize these cells. Total cellular protein was used for immunoblot analysis of various photoreceptor-specific proteins. RESULTS 661W cells grew as a monolayer and exhibited processes characteristic of neuronal cells. Immunoblot analysis showed that 661W cells expressed SV40 T antigen, blue and green cone pigments, transducin, and cone arrestin. Immunocytochemical detection of blue and green opsins showed distribution throughout the cell, the nucleus included. However, these cells did not express rod-specific antigens, such as opsin and arrestin or rod- and cone-specific proteins such as phosducin, peripherin/rds, and ROM1. Furthermore, the cells did not express RPE65, a cone- and RPE-cell-specific protein. CONCLUSIONS 661W cells demonstrate cellular and biochemical characteristics exhibited by cone photoreceptor cells. These cells also resemble neuronal cells with their spindlelike processes and should serve as a useful alternative in vitro model for the study of cone photoreceptor cell biology and associated diseases.
Cryopreservation of follicles in human ovarian cortical tissue. Comparison of serum and human serum albumin in the cryoprotectant solutions.

BACKGROUND Cryopreservation of follicles in ovarian cortical tissue has been suggested as a method for preserving fertility for young women who need to undergo cytotoxic therapy. Varying compositions of cryoprotectant solutions have been used to prevent tissue damage during cryopreservation and thawing. We compared human serum [20% (v/v)] and human serum albumin (HSA) (25 mg/ml) in cryoprotectant solutions containing propanediol and sucrose to evaluate whether serum-free medium could be used for this purpose. METHODS Biopsies of ovarian cortical tissue were obtained from 23 subjects after informed consent. Fourteen underwent Caesarean section and nine underwent sterilization by laparoscopy. The cortical tissue was cut into pieces of 1-1.5 mm(3 )and cryopreserved in cryoprotectant solutions containing serum or HSA. After thawing, a total of 1318 follicles were analysed using light microscopy, transmission electron microscopy (TEM) or live/dead assay. RESULTS Viability of the follicles was 99.3% in freshly dissected tissue. After thawing, 65% of the follicles and 75% of the oocytes were viable with serum, and 69 and 74%, respectively, with HSA. No significant differences were observed between results in solutions containing serum versus HSA. TEM showed similar results; however, poor survival of stromal tissue was evident in this analysis. The live/dead assay showed 82% viability after thawing for both groups. No benefits were seen from post-thawing culture for 4 h before histological preparation. CONCLUSIONS A cryoprotectant solution containing HSA was equally effective as one containing serum. Good viability of follicles was confirmed when using propanediol and sucrose as cryoprotectants, with a large number of follicles.
Triassic–Jurassic mass extinction as trigger for the Mesozoic radiation of crocodylomorphs

Pseudosuchia, one of the two main clades of Archosauria (Reptilia: Diapsida), suffered a major decline in lineage diversity during the Triassic–Jurassic (TJ) mass extinction (approx. 201 Ma). Crocodylomorpha, including living crocodilians and their extinct relatives, is the only group of pseudosuchians that survived into the Jurassic. We reassess changes in pseudosuchian morphological diversity (disparity) across this time interval, using considerably larger sample sizes than in previous analyses. Our results show that metrics of pseudosuchian disparity did not change significantly across the TJ boundary, contrasting with previous work suggesting low pseudosuchian disparity in the Early Jurassic following the TJ mass extinction. However, a significant shift in morphospace occupation between Late Triassic and Early Jurassic taxa is recognized, suggesting that the TJ extinction of many pseudosuchian lineages was followed by a major and geologically rapid adaptive radiation of crocodylomorphs. This marks the onset of the spectacularly successful evolutionary history of crocodylomorphs in Jurassic and Cretaceous ecosystems.
Quantum Binary Shuffled Frog Leaping Algorithm

A quantum binary shuffled frog leaping algorithm (QBSFLA) is proposed through integrating the theories of the quantum evolutionary algorithm and the shuffled frog leaping algorithm (SFLA). Firstly, the superposition state characteristic of quantum makes the separate individual expresses more states, and the probability expression characteristic makes individuals' states are expressed with certain probability for increasing the diversity of the population potentially. Then, SFLA is used to regulate the phrase of the quantum bit to achieve a balance of the local and global search and improve the run speed. The experi-mental results of three 0-1 knapsack problems solved by QBSFLA with the greedy algorithm show that QBSFLA has several advantages such as fast convergence, powerful global search ability and good stability.
A pilot study on the use of wet wraps in infants with moderate atopic eczema

Wet wrap therapy (WWT) is a well‐established treatment for severe atopic dermatitis (AD). However little evidence exists to justify widespread use in the community for less severe eczema. We compared the efficacy of WWT with a standard regime of hydrocortisone, to control moderate AD in children. We carried out a single‐observer, randomized, controlled pilot study in 19 children under 5 years of age, with AD of 30% or more body surface area, using only 1% hydrocortisone (HC) prior to the study. Group one applied HC once in the morning for 2 weeks, with wet wraps twice daily for week 1, but only at night for week 2. Group two applied HC twice daily without wet wraps. Both applied emollient twice daily and as necessary. The primary outcome measure was the Six Area, Six Sign Atopic Dermatitis (SASSAD) severity score, and the secondary outcome measures were the Infants Dermatology Quality of Life Index (IDQOL), the Dermatitis Family Impact (DFI) score and the weight of topical steroids and emollients used. Over the 2‐week active therapy period the mean fall in SASSAD was 8 [95% confidence interval (CI), −18 to +2; P = 0.11] more in the non‐WWT group, the median change in the IDQOL was 2 for Group one and 7 for Group two (95% CI for difference, −10 to +3; P = 0.24) and the median change in DFI score was 2 for Group one and 5 for Group two (95% CI for difference, −14 to +2; P = 0.42). This small study has shown that conventional therapy with HC and emollients alone is as effective as WWT for infants with moderately severe, widespread AD, and provides weak evidence to suggest that it may be more effective. We would not advocate routine use of WWT for moderate eczema without further evaluation.
Dual embryonic origin of the mammalian otic vesicle forming the inner ear

The inner ear and cochleovestibular ganglion (CVG) derive from a specialized region of head ectoderm termed the otic placode. During embryogenesis, the otic placode invaginates into the head to form the otic vesicle (OV), the primordium of the inner ear and CVG. Non-autonomous cell signaling from the hindbrain to the OV is required for inner ear morphogenesis and neurogenesis. In this study, we show that neuroepithelial cells (NECs), including neural crest cells (NCCs), can contribute directly to the OV from the neural tube. Using Wnt1-Cre, Pax3Cre/+ and Hoxb1Cre/+ mice to label and fate map cranial NEC lineages, we have demonstrated that cells from the neural tube incorporate into the otic epithelium after otic placode induction has occurred. Pax3Cre/+ labeled a more extensive population of NEC derivatives in the OV than did Wnt1-Cre. NEC derivatives constitute a significant population of the OV and, moreover, are regionalized specifically to proneurosensory domains. Descendents of Pax3Cre/+ and Wnt1-Cre labeled cells are localized within sensory epithelia of the saccule, utricle and cochlea throughout development and into adulthood, where they differentiate into hair cells and supporting cells. Some NEC derivatives give rise to neuroblasts in the OV and CVG, in addition to their known contribution to glial cells. This study defines a dual cellular origin of the inner ear from sensory placode ectoderm and NECs, and changes the current paradigm of inner ear neurosensory development.
Human Immunodeficiency Virus Type 1 Primary Isolate Neutralization Resistance Is Associated with the Syncytium-Inducing Phenotype and Lower CD4 Cell Counts in Subtype CRF01_AE-Infected Patients

ABSTRACT A number of human immunodeficiency virus type 1 (HIV-1) non-B-subtype products have been developed for present or future vaccine trials; in Thailand, several studies using subtype B and/or CRF01_AE vaccines have been conducted. To better characterize the biologic properties of these subtypes, 70 HIV-1 subtype B and E isolates were phenotyped as syncytium-inducing (SI) or non-syncytium-inducing (NSI) isolates and assessed for sensitivity to neutralizing antibody (NAb). A significantly higher number of NSI subtype E viruses were neutralization sensitive than SI subtype E viruses (P = 0.009), while no association between viral phenotype and sensitivity to NAb was observed for subtype B (P = 0.856), suggesting a difference in the neutralization patterns of subtypes B and E. Strikingly, concurrent CD4 T-cell numbers were significantly lower for subtype E-infected patients whose isolates were more resistant to NAb, both for the overall study group (P < 0.001) as well as for the 22 patients with NSI isolates (P = 0.013). Characterization of the evolution of biologic properties of both B and non-B HIV-1 subtypes will provide a clearer understanding of the repertoire of antibodies that must be elicited for a vaccine to be effective against all phenotypes and subtypes.
Deployment of multi-agent algorithms for tactical operations on UAV hardware

Small Unmanned Aerial Vehicles (UAVs) are becoming increasingly popular for tasks such as surveillance or target tracking in various types of tactical missions. Traditionally, each UAV in a mission is controlled by one or more operators. In our previous work we have developed a collection of distributed algorithms that allow one operator to control a whole team of small UAVs. Here, we report on our successful effort to deploy the developed multi-agent control algorithms to a team of hardware UAVs. To reduce costs and risk, we first developed the multi-agent control algorithms using simulated approximation of the target environment. Then, we gradually refined the model of the target environment by adding higher-fidelity models of the assets and hardware-in-the loop assets. In the final step, the algorithms were deployed and field tested in a full hardware setting and in a mixed-reality setting, where hardware UAVs are accompanied by a a number of simulated UAVs.
The association of prosomes with some of the intermediate filament networks of the animal cell [published erratum appears in J Cell Biol 1989 Mar;108(3):following 1175]

The small RNP complexes of defined morphology and biochemical composition termed prosomes, first isolated from the cytoplasm associated with repressed mRNA (Martins de Sa, C., M.-F. Grossi de Sa, O. Akhayat, F. Broders, and K. Scherrer. J. Mol. Biol. 1986. 187:47- 493), were found also in the nucleus (Grossi de Sa, M.-F., C. Martins de Sa, F. Harper, O. Coux, O. Akhayat, P. Gounon, J. K. Pal, Y. Florentin, and K. Scherrer. 1988. J. Cell Sci. 89:151-165). Immunofluorescence, immunoelectron microscopy, and immunochemical studies using mAbs directed against some of the prosomal proteins of duck erythroblasts indicate that in the cytoplasm of HeLa and PtK cells, prosome antigens are associated with the intermediate filament network of the cytokeratin type.
End-to-end solution for accessible chemical diagrams

Chemical diagrams are an important means of conveying information in chemistry and biosciences to students, starting as early as secondary school. But even in electronic teaching material, diagrams are commonly given as bitmap graphics leaving them inaccessible for visually impaired learners. We present an end-to-end solution to making these diagrams Web accessible, by employing image analysis solutions to recognise and semantically analyse diagrams, and by regenerating them in a format that makes them amenable to assistive technology. We provide software tools that allow readers to interactively engage with diagrams by exploring them step-wise and on different layers, enabling aural rendering of diagrams and their individual components together with highlighting and magnification to assist readers with low vision or learning difficulties. Our technology builds on open standards, supporting a number of computing platforms, browsers, and screen readers, and is extensible to diagrams in other STEM subjects.
Prognostic role of TET2 deficiency in myelodysplastic syndromes: A meta-analysis

Tet methylcytosine dioxygenase2 gene (TET2) is one of the most frequently mutated gene in myeloid neoplasm, but the prognostic role of TET2 aberrations in myelodysplastic syndromes (MDS) remains unclear. Therefore, we performed a meta-analysis. Fourteen eligible studies with 1983 patients were included in this meta-analysis. Among these, 2 studies evaluated the impact that the TET2 expression level had on the prognosis. The combined hazard ratios (HR) estimated for overall survival (OS) was 1.00 (95%CI: 0.74 to 1.37; p=0.989) when comparing those with TET2 mutations with those without. Among the patients treated with hypomethylating agents (HMAs) or hematopoietic stem cell transplantation (HSCT), the pooled HR for OS was 1.02 (95% CI: 0.77-1.35, p=0.89) and 1.54 (95%CI: 0.69 to 3.44; p=0.29), respectively. We also conducted an analysis of the response rate to HMAs, and the OR was 1.73 (95%CI: 1.11 to 2.70; p=0.016). Additionally, subgroup analyses showed the pooled HR for OS was 0.93(95%CI: 0.44 to 1.98; P=0.849) in WHO-classified CMML patients and 1.02(95%CI: 1.02 to 3.46; p=0.042) in studies evaluated TET2 expression level. The analysis suggested TET2 mutations had no significant prognostic value on MDS. However, the response rates to HMAs were significantly different between those with and without TET2 mutations, and the low expression level of TET2 gene was significantly associated with a poor OS in MDS patients.
Characterization of Polysaccharides with Antioxidant and Hepatoprotective Activities from the Edible Mushroom Oudemansiella radicata

The preliminary structure, in vitro antioxidant and in vivo hepatoprotective activities of water-soluble polysaccharides (ORWP) and alkali-soluble polysaccharides (ORAP), prepared from the mushroom Oudemansiella radicata, were investigated. Both ORWP and ORAP were heteropolysaccharides with mannose, glucose and galactose being the main monosaccharide components. Regarding the antioxidant activities, ORWP and ORAP showed effective 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, hydrogen peroxide scavenging activity and lipid peroxidation inhibitory effects, as well as moderate reducing power and Fe2+ chelating activity. For the hepatoprotective activity, administration of ORWP and ORAP prevented the increase in serum alanine aminotransferase and aspartate aminotransferase activities in a carbon tetrachloride-induced acute liver damage model, suppressed hepatic malondialdehyde formation and stimulated the activities of hepatic superoxide dismutase and glutathione peroxidase. Thus, we speculate that ORWP and ORAP may protect the liver from CCl4-induced hepatic damage via antioxidant mechanisms.
Methods for the Reduction of Odometry Errors in Over-Constrained Mobile Robots

This paper presents an analysis of odometry errors in over-constrained mobile robots, that is, vehicles that have more independent motors than degrees of freedom. Examples of over-constrained vehicles are the various 6-wheeled Mars Rovers like Rocky-7, Rocky-8, or Fido.Based on our analysis we developed two novel measures aimed at reducing odometry errors. We also developed a novel method that serves as a framework for the implementation of the two new measures, as well as for other, conventional error reducing measures.One of the two new measures, called “Fewest Pulses Measure,” makes use of the observation that most terrain irregularities, as well as wheel slip, result in an erroneous overcount of encoder pulses. The second new measure, called “Cross-coupled Control Measure,” optimizes the motor control algorithm of the robot to reduce synchronization errors that would otherwise result in wheel slip with conventional controllers.The novel method that serves as a framework for other measures is based on so-called “Expert Rules. ” In this paper we formulate three expert rules aimed at reducing dead-reckoning errors. Two of these expert rules are related to the foregoing discussion on error reducing measures. The third expert rule adds a gyroscope to the system and we re-examine the effectiveness of the odometry error-reducing measures in the context of this addition.In the work described in this paper we modified a Pioneer AT skid-steer platform by providing it with four independent drive motors and encoders. We implemented our error-reducing measures and the expert rule method on this over-constrained platform and present experimental results.
Incorporating lexical and prosodic information at different levels for meeting summarization

This paper investigates how prosodic features can be used to augment lexical features for meeting summarization. Automatic detection of summary-worthy content using non-lexical features, like prosody, has generally focused on features calculated over dialogue acts. However, a salient role of prosody is to distinguish important words within utterances. To examine whether including more fine grained prosodic information can help extractive summarization, we perform experiments incorporating lexical and prosodic features at different levels. For ICSI and AMI meeting corpora, we find that combining prosodic and lexical features at a lower level has better AUROC performance than adding in prosodic features derived over dialogue acts. ROUGE F-scores also show the same pattern for the ICSI data. However, the differences are less clear for the AMI data where the range of scores is much more compressed. In order to understand the relationship between the generated summaries and differences in standard measures, we look at the distribution of extracted content over meeting as well as summary redundancy. We find that summaries based on dialogue act level prosody better reflect the amount of human annotated summary content in meeting segments, while summaries derived from prosodically augmented lexical features exhibit less redundancy.
System identification without Lennart Ljung : what would have been different ?

This chapter presents a personal view on the development of identification theory in the control community, starting from the year 1965. We show how two landmark papers, (Ho and Kalman, 1965) and (Astrom and Bohlin, 1965), gave birth to two main streams of research that have dominated the development of system identification over the last fourty years. The Ho-Kalman paper gave a first solution to state-space realization theory, which led to stochastic realization, and much later to subspace identification. The Astrom-Bohlin paper laid the foundations for the highly successful Prediction Error methods based on parametric input-output models. The chapter highlights the key influence of Lennart Ljung on the development of Prediction Error Identification; it shows how his seminal contributions have profoundly changed the community’s view on identification from a search for the elusive "true system" to a goaloriented design problem.