Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Processor Allocation for Adaptively Parallel Work-Stealing Jobs

This thesis addresses the problem of scheduling multiple, concurrent, adaptively parallel jobs on a multiprogrammed shared-memory multiprocessor. Adaptively parallel jobs are jobs for which the number of processors that can be used without waste varies during execution. We focus on the specific case of parallel jobs that are scheduled using a randomized work-stealing algorithm, as is used in the Cilk multithreaded language. We begin by developing a theoretical model for two-level scheduling systems, or those in which the operating system allocates processors to jobs, and the jobs schedule their threads on the processors. To analyze the performance of a job scheduling algorithm, we model the operating system as an adversary. We show that a greedy scheduler achieves an execution time that is within a factor of 2 of optimal under these conditions. Guided by our model, we present a randomized work-stealing algorithm for adaptively parallel jobs, algorithm WSAP, which takes a unique approach to estimating the processor desire of a job. We show that attempts to directly measure a job’s instantaneous parallelism are inherently misleading. We also describe a dynamic processor-allocation algorithm, algorithm DP, that allocates processors to jobs in a fair and efficient way. Using these two algorithms, we present the design and implementation of Cilk-AP, a two-level scheduling system for adaptively parallel workstealing jobs. Cilk-AP is implemented by extending the runtime system of Cilk. We tested the Cilk-AP system on a shared-memory symmetric multiprocessor (SMP) with 16 processors. Our experiments show that, relative to the original Cilk system, Cilk-AP incurs negligible overhead and provides up to 37% improvement in throughput and 30% improvement in response time in typical multiprogramming scenarios. This thesis represents joint work with Charles Leiserson and Kunal Agrawal of the Supercomputing Technologies Group at MIT’s Computer Science and Artificial Intelligence Laboratory. Thesis Supervisor: Charles E. Leiserson Title: Professor
Color segmentation as an aid to white balancing for digital still cameras

Digital Still Cameras employ automatic white balance techniques to adjust sensor amplifier gains so that white imaged objects appear white. A color cast detection algorithm is presented that uses histogram and segmentation techniques to select near-neutral objects in the image. Once identified and classified, these objects permit determination of the scene illuminant and implicitly the respective amplifier gains. Under certain circumstances, a scene may contain no near-neutral objects. By using the segmentation operations on non-neutral image objects, memory colors, from skin, sky, and foliage objects, may be identified. If identified, these memory colors provide enough chromatic information to predict the scene illuminant. By combining the approaches from near-neutral objects with those of memory color objects, a reasonable automatic white balance over a wide range of scenes is possible.
ORAL HYGIENE AND INSTITUTIONALIZED ELDERS

The oral hygiene of institutionalized elders is poor. This population exhibits an increased risk of oral infections such as periodontal disease, caries, inflammatory mucosal disorders, and denture-related problems. Poor oral health has been associated with systemic infections, such as respiratory infections, and nutritional inadequacies. Thus the maintenance of oral health among institutionalized elders is of significant value as it has an impact on general health and quality of life. Considerable literature, however, indicates that institutionalized elders have limited access to professional oral health care services. As well, the primary caregivers, the care aides, face many barriers to providing daily oral hygiene, barriers such as time constraints and limited training in oral hygiene practices. Oral hygiene in-service training programs provided by a dental hygienist can raise the profile of oral health within the institution, support the integration of oral health care into the overall care of residents, and provide caregivers with an opportunity to be educated about daily mouth care. Dental hygienists have the education and skills that enable them to identify the oral care needs of the residents and to act as consultants for oral health policy, procedure, and program development within institutions.
Optimization of Compound Ranking for Structure‐Based Virtual Ligand Screening Using an Established FRED–Surflex Consensus Approach

The use of multiple target conformers has been applied successfully in virtual screening campaigns; however, a study on how to best combine scores for multiple targets in a hierarchic method that combines rigid and flexible docking is not available. In this study, we used a data set of 59 479 compounds to screen multiple conformers of four distinct protein targets to obtain an adapted and optimized combination of an established hierarchic method that employs the programs FRED and Surflex. Our study was extended and verified by application of our protocol to ten different data sets from the directory of useful decoys (DUD). We quantitated overall method performance in ensemble docking and compared several consensus scoring methods to improve the enrichment during virtual ligand screening. We conclude that one of the methods used, which employs a consensus weighted scoring of multiple target conformers, performs consistently better than methods that do not include such consensus scoring. For optimal overall performance in ensemble docking, it is advisable to first calculate a consensus of FRED results and use this consensus as a sub‐data set for Surflex screening. Furthermore, we identified an optimal method for each of the chosen targets and propose how to optimize the enrichment for any target.
Dermoscopy subpatterns of inflammatory skin disorders.

Plaque psoriasis (PP) and lichen ruber planus (LP) are inflammatory skin disorders that can sometimes be clinically difficult to differentiate. In these instances, punch biopsy with subsequent histopathologic evaluation is usually needed. Recently, dermoscopy has been reported to be helpful in the distinction between these 2 entities. The lesions in Figure 1 and Figure 2 were plaques located on the arms of a 53-year-old man and a 23-year-old woman, respectively. Both patients revealed only few additional lesions. Dermoscopically, the lesion in Figure 1 exhibits a network of whitish striae and red globules at the periphery (Figure 3). These dermoscopic findings raised the diagnosis of LP, whereas the multiple, uniformly sized and distributed dotted vessels, together with a central surface scale (Figure 4), led to the diagnosis of PP in the case shown in Figure 2.
Draft Genome Sequence of Non-O1 and Non-O139 Vibrio cholerae Strain VCC19

ABSTRACT Vibrio cholerae O1 is the causative agent of cholera and is ubiquitous in the aquatic environment, while V. cholerae strains non-O1 and non-O139 are recognized as causative agents of sporadic and localized outbreaks of diarrhea. Here, we report the complete sequence of a non-O1 and non-O139 V. cholerae strain (VCC19), which was isolated from the environment in Brazil. The sequence includes the integrative conjugative element (ICE). This paper is the first report of the presence of such an element in a V. cholerae strain isolated in Brazil.
Nuclear phospholipid scramblase 1 prolongs the mitotic expansion of granulocyte precursors during G‐CSF‐induced granulopoiesis

PLSCR1−/− mice exhibit normal, steady‐state hematologic parameters but impaired emergency granulopoiesis upon in vivo administration of G‐CSF. The mechanism by which PLSCR1 contributes to G‐CSF‐induced neutrophil production is largely unknown. We now report that the expansion of bone marrow myelocytes upon in vivo G‐CSF treatment is reduced in PLSCR1−/− mice relative to WT. Using SCF‐ER‐Hoxb8‐immortalized myeloid progenitors to examine the progression of G‐CSF‐driven granulocytic differentiation in vitro, we found that PLSCR1 prolongs the period of mitotic expansion of proliferative granulocyte precursors, thereby giving rise to increased neutrophil production from their progenitors. This effect of PLSCR1 is blocked by a ΔNLS‐PLSCR1, which prevents its nuclear import. By contrast, mutation that prevents the membrane association of PLSCR1 has minimal impact on the role of PLSCR1 in G‐CSF‐induced granulopoiesis. These data imply that the capacity of PLSCR1 to augment G‐CSF‐dependent production of mature neutrophils from myeloid progenitors is unrelated to its reported activities at the endofacial surface of the plasma membrane but does require entry of the protein into the nucleus, suggesting that this response is mediated through the observed effects of PLSCR1 on gene transcription.
Optimal Feature Set for Automatic Detection and Classification of Underwater Objects in SAS Images

The problem of automatic detection and classification for mine hunting applications is addressed. We propose a set of algorithms which are tested using a large database of real synthetic aperture sonar (SAS) images. The highlights and shadows of the objects in an SAS image are segmented using both a Markovian algorithm and the active contours algorithm. The comparison of both segmentation results is used as a feature for classification. In addition, other features are considered. These include geometrical shape descriptors, not only of the shadow region, but also of the object highlight, which demonstrates a significant improvement of the performance. Furthermore, a novel set of features based on the image statistics is described. Finally, we propose an optimal feature set that leads to the best classification results for the available database.
Reduced gray matter volume in normal adults with a maternal family history of Alzheimer disease

Objective: A consistently identified risk factor for Alzheimer disease (AD) is family history of dementia, with maternal transmission significantly more frequent than paternal transmission. A history of maternal AD may be related to AD-like glucose consumption in cognitively healthy subjects. In this cross-sectional study, we tested whether cognitively healthy people with a family history of AD have less gray matter volume (GMV), an endophenotype for late-onset AD, than individuals with no family history, and whether decreases in GMV are different in subjects with a maternal family history. Methods: As part of the Kansas University Brain Aging Project, 67 cognitively intact individuals with a maternal history of late-onset AD (FHm, n = 16), a paternal history of AD (FHp, n = 8), or no parental history of AD (FH−, n = 43), similar in age, gender, education, and Mini-Mental State Examination score, were scanned at 3 T. We used voxel-based morphometry to examine GMV differences between groups, controlling for age, gender, and apoE4. Results: Cognitively healthy individuals with a family history of late-onset AD had significantly decreased GMV in the precuneus, middle frontal, inferior frontal, and superior frontal gyri compared with FH− individuals. FHm subjects had significantly smaller inferior frontal, middle frontal, precuneus, and lingual gyri compared with FH− and FHp subjects. Conclusions: Overall, maternal family history of Alzheimer disease (AD) in cognitively normal individuals is associated with lower gray matter volume in AD-vulnerable brain regions. These data complement and extend reports of cerebral metabolic differences in subjects with a maternal family history.
Telmisartan lowers albuminuria in type 2 diabetic patients treated with angiotensin enzyme inhibitors.

PURPOSE Angiotensin-converting-enzyme inhibitors (ACEIs) provide renal protection in patients with type 2 diabetes and microalbuminuria. MATERIAL AND METHODS In the presented study we followed 34 stable, type 2 diabetic patients with persistent albuminuria treated with maximal doses of ACEIs as a part of their anti-hypertensive treatment. Telmisartan--an angiotensin receptor blocker (ARB)--in a dose of 40 mg was added to the treatment and the patients were observed for 12 weeks. We measured creatinine clearance, 24-hour urinary albumin excretion, before and after 12 weeks of combined therapy. RESULTS The addition of telmisartan resulted in a significant reduction of albuminuria from median 157 to 67 mg/24h. No change in creatinine clearance was observed (93 vs 97 ml/min). CONCLUSION The addition of telmisartan to a maximum dose of ACEI is safe and results in further albuminuria decrease in patients with type 2 diabetes and incipient nephropathy.
Sorting and Selection with Imprecise Comparisons

We consider a simple model of imprecise comparisons: there exists some δ > 0 such that when a subject is given two elements to compare, if the values of those elements (as perceived by the subject) differ by at least δ, then the comparison will be made correctly; when the two elements have values that are within δ, the outcome of the comparison is unpredictable. This model is inspired by both imprecision in human judgment of values and also by bounded but potentially adversarial errors in the outcomes of sporting tournaments. Our model is closely related to a number of models commonly considered in the psychophysics literature where δ corresponds to the Just Noticeable Difference (JND) unit or difference threshold. In experimental psychology, the method of paired comparisons was proposed as a means for ranking preferences among n elements of a human subject. The method requires performing all (n2) comparisons, then sorting elements according to the number of wins. The large number of comparisons is performed to counter the potentially faulty decision-making of the human subject, who acts as an imprecise comparator. We show that in our model the method of paired comparisons has optimal accuracy, minimizing the errors introduced by the imprecise comparisons. However, it is also wasteful because it requires all (n2). We show that the same optimal guarantees can be achieved using 4n3/2 comparisons, and we prove the optimality of our method. We then explore the general tradeoff between the guarantees on the error that can be made and number of comparisons for the problems of sorting, max-finding, and selection. Our results provide strong lower bounds and close-to-optimal solutions for each of these problems.
Searching for new strategies against polymicrobial biofilm infections: guanylated polymethacrylates kill mixed fungal/bacterial biofilms.

OBJECTIVES Biofilm-related human infections have high mortality rates due to drug resistance. Cohabitation of diverse microbes in polymicrobial biofilms is common and these infections present additional challenges for treatment compared with monomicrobial biofilms. Here, we address this therapeutic gap by assessing the potential of a new class of antimicrobial agents, guanylated polymethacrylates, in the treatment of polymicrobial biofilms built by two prominent human pathogens, the fungus Candida albicans and the bacterium Staphylococcus aureus. METHODS We used imaging and quantitative methods to test the antibiofilm efficacy of guanylated polymethacrylates, a new class of drugs that structurally mimic antimicrobial peptides. We further compared guanylated polymethacrylates with first-line antistaphylococcal and anti-Candida agents used as combinatorial therapy against polymicrobial biofilms. RESULTS Guanylated polymethacrylates were highly effective as a sole agent, killing both C. albicans and S. aureus when applied to established polymicrobial biofilms. Furthermore, they outperformed multiple combinations of current antimicrobial drugs, with one of the tested compounds killing 99.98% of S. aureus and 82.2% of C. albicans at a concentration of 128 mg/L. The extracellular biofilm matrix provided protection, increasing the MIC of the polymethacrylates by 2-4-fold when added to planktonic assays. Using the C. albicans bgl2ΔΔ mutant, we implicate matrix polysaccharide β-1,3 glucan in the mechanism of protection. Data for two structurally distinct polymers suggest that this mechanism could be minimized through chemical optimization of the polymer structure. Finally, we demonstrate that a potential application for these polymers is in antimicrobial lock therapy. CONCLUSIONS Guanylated polymethacrylates are a promising lead for the development of an effective monotherapy against C. albicans/S. aureus polymicrobial biofilms.
Vertex disjoint equivalent subgraphs of order 3

Let k be a fixed integer at least 3. It is proved that every graph of order (2k − 1 − 1/k)n + O(1) contains n vertex disjoint induced subgraphs of order k such that these subgraphs are equivalent to each other and they are equivalent to one of four graphs: a clique, an independent set, a star, or the complement of a star. In particular, by substituting 3 for k, it is proved that every graph of order 14n/3 + O(1) contains n vertex disjoint induced subgraphs of order 3 such that they are equivalent to each other. © 2007 Wiley Periodicals, Inc. J Graph Theory 56: 159–166, 2007
Homonymous hemianopia: challenges and solutions

Stroke is the most common cause of homonymous hemianopia (HH) in adults, followed by trauma and tumors. Associated signs and symptoms, as well as visual field characteristics such as location and congruity, can help determine the location of the causative brain lesion. HH can have a significant effect on quality of life, including problems with driving, reading, or navigation. This can result in decreased independence, inability to enjoy leisure activities, and injuries. Understanding these restrictions, as well as the management options, can aid in making the best use of remaining vision. Treatment options include prismatic correction to expand the remaining visual field, compensatory training to improve visual search abilities, and vision restoration therapy to improve the vision itself. Spontaneous recovery can occur within the first months. However, because spontaneous recovery does not always occur, methods of reducing visual disability play an important role in the rehabilitation of patients with HH.
Kaplan–Meier curves for survivor causal effects with time-to-event outcomes

Background In clinical trials, an outcome of interest may be undefined for individuals who die before the outcome is evaluated. One approach to deal with such issues is to consider the survivor causal effect (SCE), which is defined as the effect of treatment on the outcome among the subpopulation that would have survived under either treatment arm. Although several methods have been presented to estimate the SCE with time-to-event outcomes, they are difficult to implement in practice. Purpose We present a simple method to create Kaplan–Meier curves and to estimate the hazard ratio (HR) for the SCE with time-to-event outcomes. Methods To develop such a method, we applied the weighted average method presented for the SCE to outcomes with no censoring, where weights are calculated using the probability that a patient would have survived had the patient been in the other treatment arm. By multiplying the weight to each patient, Kaplan–Meier curves can be created for the SCE to outcomes with censoring. The HR is then calculated using a weighted proportional hazard model. For this method, two assumptions need to be introduced to achieve unbiasedness. Results The proposed method is illustrated using data from a randomized Phase II clinical trial, comparing two chemotherapy treatments with radiotherapy in patients with esophageal cancer. Here, we focus on the loco-regional control rate, which is calculated from the time after randomization until recurrence in the radiation field. The duration is undefined for patients who died without recurrence. The proposed method yielded a HR of 1.026 (95% confidence interval (CI): 0.627, 1.677). The standard method, where data of patients who died without progression were regarded as censored at the time of death, yielded a HR of 1.121 (95% CI: 0.688, 1.827). Limitations The proposed method requires two assumptions. As a general problem, unfortunately, whether these assumptions hold cannot be confirmed from the observed data. Thus, we cannot confirm whether the Kaplan–Meier curves and the HR are unbiased. Conclusion We have proposed a simple method for the SCE with time-to-event outcomes, which is easy to implement in practice. The proposed method is a potentially valuable supplement to the standard method.
l‐Type amino acid transporter 1 inhibitors inhibit tumor cell growth

Most tumor cell membranes overexpress l‐type amino acid transporter 1, while normal cell membranes contain l‐type amino acid transporter 2; both are Na+‐independent amino acid transporters. Therefore, compounds that selectively inhibit l‐type amino acid transporter 1 offer researchers with a novel cancer molecular target. Synthetic chemistry efforts and in vitro screening have produced a variety of novel compounds possessing high in vitrol‐type amino acid transporter 1 selectivity; KYT‐0353 was one such compound. The present studies illustrate that KYT‐0353 inhibited 14C‐leucine uptake and cell growth in human colon cancer‐derived HT‐29 cells; IC50s were 0.06 μm and 4.1 μm, respectively. KYT‐0353 also inhibited 14C‐leucine uptake in mouse renal proximal tubule cells expressing l‐type amino acid transporter 1, and inhibited cell growth; IC50s were 0.14 μm and 16.4 μm, respectively. Compared to control animals, intravenously administered KYT‐0353 (12.5 mg/kg and 25.0 mg/kg) showed statistically significant growth inhibition against HT‐29 tumors transplanted to nude mice with maximal inhibition ratios of 65.9% and 77.2%, respectively. Body weight increase with time – a safety indicator – was slightly depressed at 12.5 mg/kg and 25.0 mg/kg with maximal ratios of 3.7% (day 2) and 6.3% (day 11), respectively. Thus, KYT‐0353 showed significant growth inhibitory effects on HT‐29 cells both in vitro and in vivo, whereas it only caused a slight body weight depression. Therefore, KYT‐0353 appears to have potential as a novel anti‐tumor agent, presumably via selective in vivol‐type amino acid transporter 1 inhibition. (Cancer Sci 2009)
An Efficient Earth Mover's Distance Algorithm for Robust Histogram Comparison

We propose EMD-L1: a fast and exact algorithm for computing the earth mover's distance (EMD) between a pair of histograms. The efficiency of the new algorithm enables its application to problems that were previously prohibitive due to high time complexities. The proposed EMD-L1 significantly simplifies the original linear programming formulation of EMD. Exploiting the L1 metric structure, the number of unknown variables in EMD-L1 is reduced to O(N) from O(N2) of the original EMD for a histogram with N bins. In addition, the number of constraints is reduced by half and the objective function of the linear program is simplified. Formally, without any approximation, we prove that the EMD-L1 formulation is equivalent to the original EMD with a L1 ground distance. To perform the EMD-L1 computation, we propose an efficient tree-based algorithm, Tree-EMD. Tree-EMD exploits the fact that a basic feasible solution of the simplex algorithm-based solver forms a spanning tree when we interpret EMD-L1 as a network flow optimization problem. We empirically show that this new algorithm has an average time complexity of O(N2), which significantly improves the best reported supercubic complexity of the original EMD. The accuracy of the proposed methods is evaluated by experiments for two computation-intensive problems: shape recognition and interest point matching using multidimensional histogram-based local features. For shape recognition, EMD-L1 is applied to compare shape contexts on the widely tested MPEG7 shape data set, as well as an articulated shape data set. For interest point matching, SIFT, shape context and spin image are tested on both synthetic and real image pairs with large geometrical deformation, illumination change, and heavy intensity noise. The results demonstrate that our EMD-L1-based solutions outperform previously reported state-of-the-art features and distance measures in solving the two tasks