Miracle-dz/UniFAR-FTUs huggingface dataset:
If Not Turing's Test, Then What?

If it is true that good problems produce good science, then it will be worthwhile to identify good problems, and even more worthwhile to discover the attributes that make them good problems. This discovery process is necessarily empirical, so we examine several challenge problems, beginning with Turing's famous test, and more than a dozen attributes that challenge problems might have. We are led to a contrast between research strategies -- the successful "divide and conquer" strategy and the promising but largely untested "developmental" strategy -- and we conclude that good challenge problems encourage the latter strategy.
Genistein Suppresses Spontaneous Oviduct Tumorigenesis in Quail

Spontaneous leiomyomas of the oviduct are common tumors of the Japanese quail (Coturnix coturnix japonica) and laying hens. This makes it a good animal model for screening potential agents for testing in the prevention and treatment of human myoma uteri. Genistein has been shown to inhibit the growth of various cancer cells. We investigated the effects of genistein supplementation on the development of fibroid tumors in the oviduct, serum oxidative stress markers [malondialdehyde (MDA), 8-isoprostane, 4-hydroxyalkenal (HAE), 8-hydroxy-2′ -deoxyguanosine (8-OHdG) levels], soy isoflavone levels, and tissue biomarkers [Connexin 43 (Cx43), Bcl-2, and Bax and heat shock protein 70 (Hsp70) expression] in Japanese quail. One hundred and fifty quail (12 mo old) were assigned to 3 experimental groups as 5 replicates of pens containing 10 birds in each. Birds were fed either a basal diet or the basal diet supplemented with 400 mg or 800 mg of genistein/kg of diet. The animals were sacrificed after 315 days, and the tumors were identified. Genistein supplementation significantly decreased the incidence of fibroid tumors as compared to control birds (P = 0.04). The tumors in genistein-fed birds were smaller than those found in control birds (P = 0.02). Serum MDA, 8-isoprostane, and HAE levels were lower in treatment groups than in control group (MDA: 2.01 vs. 0.82; 8-isoprostane: 135 vs. 101; HAE: 1.45 vs. 0.73; P ≤ 0.01). The concentrations of serum 8-OHdG, which is a marker of oxidative damage, in the groups were 27.5, 22.4, and 21.3 ng/ml, respectively (P = 0.05). The expression of cell cycle regulatory proteins, Bcl-2, was 4.18 and 4.61 in the genistein groups and 6.21 in the control group, and the expression of Bax was 10.93 and 16.78 in the genistein groups and 7.60 in the control group (P < 0.001 for Bax). Cx43 level was 2.56 and 2.40 in the genistein groups compared with 5.15 in the control group. None of the differences in the Cx43 and Bcl-2 of the groups were significant. The expression of heat shock proteins, Hsp60 and Hsp70, were not different between groups, although Hsp70 level of the genistein groups (19.73) was lower than the control group (27.8). The results indicate that dietary supplementation of genistein reduces the incidence and size of spontaneously occurring leiomyoma of the oviduct in the Japanese quail. Clinical trials should be conducted to investigate the efficacy of genistein supplementation in the prevention and treatment of uterine leiomyoma in humans.
Aflatoxin-Contaminated Nut Separation by Applied Machinery and Processing Stages in Fresh Pistachio Processing Plant

In pistachio nuts, aflatoxin is mainly concentrated in the green hull-cracked nuts in the orchard even prior to harvest. However, during the hull-removal process, the hulls of all nuts including the cracked, identifiable nuts are removed causing an important characterization criterion of the contaminated nuts, to be lost. This, in turn, makes it harder to detect the contaminated nuts. However, during the processing stage, there is a good possibility of sorting the contaminated nuts based on their other inherent features, such as specific gravity and stain on the hard shell. In this study, we aimed to explore the effect of applied processing machinery and related sequences in the aflatoxin flow during post-harvest processing and the possible ways of reducing aflatoxin contamination in the Iranian pistachio industry. We planned a systematic sampling from the main and reject streams in two major prevailing processing methods, namely, wet and dry. In the dry processing method, the reject streams such as the adhering-hull rejects, air floaters, and manual hand pick-outs from the final inspection were found to be significantly more contaminated than the main stream. However, in the wet processing method, the input stream was considered highly contaminated. Among the sorting stages, only the adhering-hull rejects of the sinkers were considered more contaminated than the main stream. A contamination removal index was developed and applied to compare the effectiveness of the processing procedures. The water flotation tank was deemed responsible for 52.5% of aflatoxin contamination removal compared to 2.1% in the air flotation system. More effective sorting was achieved by the adhering-hull remover, which was preceded by a rubber-drum huller instead of the metal-drum type. Thus, by combining the most effective techniques of aflatoxin removal, an improved and more efficient method may be designed for pistachio processing plants.
Potent and selective inhibitors of Akt kinases slow the progress of tumors in vivo

The Akt kinases are central nodes in signal transduction pathways that are important for cellular transformation and tumor progression. We report the development of a series of potent and selective indazole-pyridine based Akt inhibitors. These compounds, exemplified by A-443654 (Ki = 160 pmol/L versus Akt1), inhibit Akt-dependent signal transduction in cells and in vivo in a dose-responsive manner. In vivo, the Akt inhibitors slow the progression of tumors when used as monotherapy or in combination with paclitaxel or rapamycin. Tumor growth inhibition was observed during the dosing interval, and the tumors regrew when compound administration was ceased. The therapeutic window for these compounds is narrow. Efficacy is achieved at doses ∼2-fold lower than the maximally tolerated doses. Consistent with data from knockout animals, the Akt inhibitors induce an increase in insulin secretion. They also induce a reactive increase in Akt phosphorylation. Other toxicities observed, including malaise and weight loss, are consistent with abnormalities in glucose metabolism. These data show that direct Akt inhibition may be useful in cancer therapy, but significant metabolic toxicities are likely dose limiting.
Forgive Us our SYNs: Technical and Ethical Considerations for Measuring Internet Filtering

We provide an overview of technical and ethical considerations for measuring Internet filtering, focusing on client-side and network side channel techniques. Client-side measurements are any measurement that relies on software deployed on a network vantage point. Users are typically involved in installing and running the measurement software, and informed consent process to ensure users are aware of risks in doing so should be followed. However, the relative risk is highly contextually specific, and can vary depending on the location and background of the user running the measurement. Network side channel techniques do not require installation of special software. These techniques send packets to machines such as SYNs or pings with spoofed source addresses to cause those machines to automatically send responses to the spoofed addresses. By taking advantage of the common implementation details of many network stacks, these techniques can measure whether the responses were received by the machine at the spoofed address by exploiting the way that information flows throughout these machines' stacks. It is impractical to obtain prior informed consent for network side channel experiments. These techniques are interventions into an environment, and to be done responsibly research risk has to reduced to a minimum. We identify open questions these distinct approaches raise and discuss possible mitigations for ensuring responsible network measurement experiments.
Body morphology differs in wild juvenile Chinook salmon Oncorhynchus tshawytscha that express different migratory phenotypes in the Willamette River, Oregon, U.S.A.

Body morphology of juvenile Chinook salmon Oncorhynchus tshawytscha in the upper Willamette River, Oregon, U.S.A. , was analysed to determine if variation in body shape is correlated with migratory life-history tactics followed by juveniles. Body shape was compared between migrating juveniles that expressed different life-history tactics, i.e. autumn migrants and yearling smolts, and among parr sampled at three sites along a longitudinal river gradient. In the upper Willamette River, the expression of life-history tactics is associated with where juveniles rear in the basin with fish rearing in downstream locations generally completing ocean ward migrations earlier in life than fish rearing in upstream locations. The morphological differences that were apparent between autumn migrants and yearling smolts were similar to differences between parr rearing in downstream and upstream reaches, indicating that body morphology is correlated with life-history tactics. Autumn migrants and parr from downstream sampling sites had deeper bodies, shorter heads and deeper caudal peduncles compared with yearling smolts and parr from the upstream sampling site. This study did not distinguish between genetic and environmental effects on morphology; however, the results suggest that downstream movement of juveniles soon after emergence is associated with differentiation in morphology and with the expression of life-history variation.
Out-of-Sequence Traffic Classification Based on Improved Dynamic Time Warping

SUMMARY Tra ﬃ c classiﬁcation has recently gained much attention in both academic and industrial research communities. Many machine learning methods have been proposed to tackle this problem and have shown good results. However, when applied to tra ﬃ c with out-of-sequence packets, the accuracy of existing machine learning approaches decreases dramatically. We observe the main reason is that the out-of-sequence packets change the spatial representation of feature vectors, which means the property of linear mapping relation among features used in machine learning approaches cannot hold any more. To address this problem, this paper proposes an Improved Dynamic Time Warping (IDTW) method, which can align two feature vectors using non-linear alignment. Experimental results on two real traces show that IDTW achieves better classiﬁcation accuracy in out-of-sequence tra ﬃ c classiﬁcation, in comparison to existing machine learning approaches.
Gelsolin has three actin-binding sites

Gelsolin, a Ca2+-modulated actin filament-capping and -severing protein, complexes with two actin monomers. Studies designed to localize binding sites on proteolytic fragments identify three distinct actin-binding peptides. 14NT, a 14-kD fragment that contains the NH2 terminal, will depolymerize F-actin. This peptide forms a 1:1 complex with G-actin which blocks the exchange of etheno-ATP from bound actin. The estimated association and dissociation rates for this complex are 0.3 microM-1 s-1 and 1.35 x 10(-6) s-1 which gives a maximum calculated Kd = 4.5 x 10(-12) M. 26NT, the adjacent peptide on the NH2-terminal half of gelsolin, binds to both G- and F-actin. This fragment has little or no intrinsic severing activity and will bind to F-actin to nearly stoichiometric ratios. The interactions of 14NT and 26NT with actin are largely Ca2+ independent and one of these sites, probably 14NT, is the EGTA-stable site identified in the intact protein. 41CT, the COOH-terminal half of gelsolin, forms a rapidly reversible 1:1 complex with actin, Kd = 25 nM, that slows but does not block etheno- ATP exchange. This interaction is Ca2+ dependent and is the exchangeable site in the intact protein. One of these sites is hidden in the intact protein, but cleavage into half fragments exposes all three and removes the Ca2+ dependence of severing.
Distributed and Centralized Hybrid CSMA/CA-TDMA Schemes for Single-Hop Wireless Networks

The strength of carrier-sense multiple access with collision avoidance (CSMA/CA) can be combined with that of time-division multiple access (TDMA) to enhance the channel access performance in wireless networks such as the IEEE 802.15. 4-based wireless personal area networks. In particular, the performance of legacy CSMA/CA-based medium access control scheme in congested networks can be enhanced through a hybrid CSMA/CA-TDMA scheme while preserving the scalability property. In this paper, we present distributed and centralized channel access models that follow the transmission strategies based on Markov decision process (MDP) to access both contention period and contention-free period in an intelligent way. The models consider the buffer status as an indication of congestion provided that the offered traffic does not exceed the channel capacity. We extend the models to consider the hidden node collision problem encountered due to the signal attenuation caused by channel fading. The simulation results show that the MDP-based distributed channel access scheme outperforms the legacy slotted CSMA/CA scheme. The centralized model outperforms the distributed model but requires the global information of the network.
Toward a Critical Pedagogy of Popular Culture: Literacy Development among Urban Youth.

Finding effective ways to teach today’s student population is perhaps the greatest challenge facing literacy educators in the United States. As classrooms become increasingly diverse, educators struggle to find curricula and pedagogical strategies that are inclusive and affirmative yet facilitate the development of academic and critical literacies. Unfortunately, much of the multicultural education literature—with its limited conception of culture as a racial or ethnic identity—offers little to help teachers attempting to make connections and create learning communities in multiethnic urban classrooms (McCarthy, 1998). New approaches, such as the critical teaching of popular culture, can help students acquire and develop the literacies needed to navigate “newcentury” schools. Popular culture can help students deconstruct dominant narratives and contend with oppressive practices in hopes of achieving a more egalitarian and inclusive society.
Mechanistic Approach to Stability Studies as a Tool for the Optimization and Development of New Products Based on L. rhamnosus Lcr35® in Compliance with Current Regulations

Probiotics are of great current interest in the pharmaceutical industry because of their multiple effects on human health. To beneficially affect the host, an adequate dosage of the probiotic bacteria in the product must be guaranteed from the time of manufacturing to expiration date. Stability test guidelines as laid down by the ICH-Q1A stipulate a minimum testing period of 12 months. The challenge for producers is to reduce this time. In this paper, a mechanistic approach using the Arrhenius model is proposed to predict stability. Applied for the first time to laboratory and industrial probiotic powders, the model was able to provide a reliable mathematical representation of the effects of temperature on bacterial death (R2>0.9). The destruction rate (k) was determined according to the manufacturing process, strain and storage conditions. The marketed product demonstrated a better stability (k = 0.08 months−1) than the laboratory sample (k = 0.80 months−1). With industrial batches, k obtained at 6 months of studies was comparable to that obtained at 12 months, evidence of the model’s robustness. In addition, predicted values at 12 months were greatly similar (±30%) to those obtained by real-time assessing the model’s reliability. This method could be an interesting approach to predict the probiotic stability and could reduce to 6 months the length of stability studies as against 12 (ICH guideline) or 24 months (expiration date).
Altered biologic activities of commercial polychlorinated biphenyl mixtures after microbial reductive dechlorination.

The reductive dechlorination of polychlorinated biphenyls (PCBs) by anaerobic bacteria has recently been established as an important environmental fate of these compounds. This process removes chlorines directly from the biphenyl ring with replacement by hydrogen, resulting in a product mixture in which the average number of chlorines per biphenyl is reduced. In this study, dechlorination of commercial PCB mixtures (Aroclors 1242 and 1254) by microorganisms eluted from PCB-contaminated sediments of the River Raisin (Michigan) and Silver Lake (Massachusetts) caused a depletion in the proportion of highly chlorinated PCB congeners and an accumulation of lesser-chlorinated congeners. Dechlorination occurred primarily at the meta and, to a much lesser extent, para positions of biphenyl. The concentrations of the coplanar congeners including 3,3',4,4',5-pentachlorobiphenyl, the most potent dioxinlike congener, were significantly lowered by reductive dechlorination. Microbial reductive dechlorination of commercial PCB mixtures caused a substantial reduction in biologic activities in several instances. It significantly lowered or eliminated the inhibitory effects of Aroclors on fertilization of mouse gametes in vitro. Similarly, the dechlorinated product mixtures had substantially lower ethoxyresorufin-O-deethylase induction potencies and showed less ability to induce activating protein 1 transcription factor activity as compared to the unaltered Aroclors. In other assays the same dechlorinated product mixtures demonstrated biologic activities similar to the nondechlorinated Aroclors, including the ability of PCB mixtures to stimulate insulin secretion and cause neutrophil activation. The data presented here establish that the biologic activities of commercial PCB mixtures are altered by microbial reductive dechlorination and that an assessment of their toxic potential requires an array of tests that include the different mechanisms associated with PCBs. ImagesFigure 2Figure 3Figure 4Figure 5Figure 6
Young age and pathological features predict breast cancer outcome - report from a dual Institution experience in Serbia.

PURPOSE The aim of this study was to investigate the influence of clinicopathological and biological characteristics on prognosis, disease free survival (DFS) and overall survival (OS), of very young patients (≤35 years of age) with breast cancer. METHODS We retrospectively collected information of 150 women diagnosed with breast cancer, aged ≤35 years, who were operated and treated at two University Hospitals in Serbia between January 2009 and February 2011. RESULTS After a median follow up of 44 months patients ≤30 had shorter DFS and OS compared to patients aged 31-35 years (p=0.004 and p=0.037, respectively). The differences in DFS and OS were significant with decreased survival associated with higher tumor grade (p=0.005 and p=0.0001, respectively). Tumor size and number of positive nodes were predictors of outcome with decreased survival associated with higher tumor size (p=0.0019 for DFS and p<0.0001 for OS) and increasing number of nodes (p<0.0001 for both). HER 2 receptor did not seem to have a prognostic influence while patients with hormonal receptors (HRs) positive tumors had a better DFS (p=0.034) and OS (p=0.046) than those with HRs negative tumors. In univariate survival analysis, a significant difference in DFS (p=0.0003) and OS (p=0.0003) was found between patients with vs without lymphovascular invasion (LVI). CONCLUSION Diagnosis of breast cancer at very young age (<30) was associated with increased risk of death and shorter DFS than women aged 31-35. Negative impact on survival was seen in patients with presence of LVI, negative HRs and higher grade and stage at the time of presentation.
In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader

Definitive secondary structural mapping of RNAs in vitro can be complicated by the presence of more than one structural conformer or multimerization of some of the molecules. Until now, probing a single structure of conformationally flexible RNA molecules has typically relied on introducing stabilizing mutations or adjusting buffer conditions or RNA concentration. Here, we present an in-gel SHAPE (selective 2′OH acylation analysed by primer extension) approach, where a mixed structural population of RNA molecules is separated by non-denaturing gel electrophoresis and the conformers are individually probed within the gel matrix. Validation of the technique using a well-characterized RNA stem-loop structure, the HIV-1 trans-activation response element, showed that authentic structure was maintained and that the method was accurate and highly reproducible. To further demonstrate the utility of in-gel SHAPE, we separated and examined monomeric and dimeric species of the HIV-1 packaging signal RNA. Extensive differences in acylation sensitivity were seen between monomer and dimer. The results support a recently proposed structural switch model of RNA genomic dimerization and packaging, and demonstrate the discriminatory power of in-gel SHAPE.
Musculoskeletal fitness and risk of mortality.

PURPOSE To quantify the relationship between musculoskeletal fitness and all-cause mortality in the Canadian population. METHODS The sample consisted of 8116 people (3933 men and 4183 women), aged 20-69 yr, who participated in the 1981 Canada Fitness Survey. Measures of musculoskeletal fitness included sit-ups, push-ups, grip strength, and sit-and-reach trunk flexibility. In the 13 yr after the Canada Fitness Survey, there were 238 deaths and a total of 101,685 person-years. Proportional hazards regression was used to estimate the risk of mortality across baseline age- and sex-specific quartiles of the musculoskeletal fitness measures. All models included the effects of age, smoking status, body mass, and estimated VO2max as covariates, and the upper quartile was set as the reference group. RESULTS There was no pattern of increased risk of mortality across quartiles of trunk flexibility or push-ups; however, there was a significantly higher risk in the lower quartile of sit-ups in both men (relative risk (RR) = 2.72, 95% CI 1.56-4.64) and women (RR = 2.26, 95% CI 1.15-4.43). Grip strength was not predictive of mortality in women, although there was a 49% increased risk of death in the lower quartile of grip strength in males (RR = 1.49, 95% CI 0.86-2.59). CONCLUSION The results suggest that some components of musculoskeletal fitness, particularly sit-ups (abdominal muscular endurance), are predictive of mortality in the Canadian population.
Continuation-based partial evaluation

Binding-time improvements aim at making partial evaluation (a.k.a. program specialization) yield a better result. They have been achieved so far mostly by hand-transforming the source program. We observe that as they are better understood, these hand-transformations are progressively integrated into partial evaluators, thereby alleviating the need for source-level binding-time improvements. Control-based binding-time improvements, for example, follow this pattern: they have evolved from ad-hoc source-level rewrites to a systematic source-level transformation into continuation-passing style (CPS). Recently, Bondorf has explicitly integrated the CPS transformation into the specializer, thus partly alleviating the need for source-level CPS transformation. This CPS integration is remarkably effective but very complex and goes beyond a simple CPS transformation. We show that it can be achieved directly by using the control operators shift and reset, which provide access to the current continuation as a composable procedure. We automate, reproduce, and extend Bondorf's results, and describe how this approach scales up to hand-writing partial-evaluation compilers. The first author has used this method to bootstrap the new release of Consel's partial evaluator Schism. The control operators not only allow the partial evaluator to remain in direct style, but also can speed up partial evaluation significantly.