Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluid dynamics of feeding behaviour in white-spotted bamboo sharks

SUMMARY Although the motor control of feeding is presumed to be generally conserved, some fishes are capable of modulating the feeding behaviour in response to prey type and or prey size. This led to the `feeding modulation hypothesis', which states that rapid suction strikes are pre-programmed stereotyped events that proceed to completion once initiated regardless of sensory input. If this hypothesis holds true, successful strikes should be indistinguishable from unsuccessful strikes owing to a lack of feedback control in specialized suction feeding fishes. The hydrodynamics of suction feeding in white-spotted bamboo sharks (Chiloscyllium plagiosum) was studied in three behaviours: successful strikes, intraoral transports of prey and unsuccessful strikes. The area of the fluid velocity region around the head of feeding sharks was quantified using time-resolved digital particle image velocimetry (DPIV). The maximal size of the fluid velocity region is 56% larger in successful strikes than unsuccessful strikes (10.79 cm2 vs 6.90 cm2), but they do not differ in duration, indicating that strikes are modulated based on some aspect of the prey or simply as a result of decreased effort on the part of the predator. The hydrodynamic profiles of successful and unsuccessful strikes differ after 21 ms, a period probably too short to provide time to react through feedback control. The predator-to-prey distance is larger in missed strikes compared with successful strikes, indicating that insufficient suction is generated to compensate for the increased distance. An accuracy index distinguishes unsuccessful strikes (–0.26) from successful strikes (0.45 to 0.61). Successful strikes occur primarily between the horizontal axis of the mouth and the dorsal boundary of the ingested parcel of water, and missed prey are closer to the boundary or beyond. Suction transports are shorter in duration than suction strikes but have similar maximal fluid velocity areas to move the prey through the oropharyngeal cavity into the oesophagus (54 ms vs 67 ms).
MEK , p 38 , and PI-3 K mediate cross talk between EGFR and TNFR in enhancing hepatocyte growth factor production from human mesenchymal stem cells

Wang Y, Weil BR, Herrmann JL, Abarbanell AM, Tan J, Markel TA, Kelly ML, Meldrum DR. MEK, p38, and PI-3K mediate cross talk between EGFR and TNFR in enhancing hepatocyte growth factor production from human mesenchymal stem cells. Am J Physiol Cell Physiol 297: C1284–C1293, 2009. First published August 19, 2009; doi:10.1152/ajpcell.00183. 2009. —Human bone marrow mesenchymal stem cells (MSCs) are a potent source of growth factors, which are partly responsible for their beneficial paracrine effects. We reported previously that transforming growth factor(TGF), a putative mediator of wound healing and the injury response, increases the release of vascular endothelial growth factor (VEGF), augments tumor necrosis factor(TNF)-stimulated VEGF production, and activates mitogen-activated protein kinases and phosphatidylinositol 3-kinase (PI-3K) pathway in human MSCs. The experiments described in this report indicate that TGFincreases MSC-derived hepatocyte growth factor (HGF) production. TGF-stimulated HGF production was abolished by inhibition of MEK, p38, PI-3K, or by small interfering RNA (siRNA) targeting TNF receptor 2 (TNFR2), but was not attenuated by siRNA targeting TNF receptor 1 (TNFR1). Ablation of TNFR1 significantly increased basal and stimulated HGF. A potent synergy between TGFand TNFwas noted in MSC HGF production. This synergistic effect was abolished by MEK, P38, PI-3K inhibition, or by ablation of both TNF receptors using siRNA. We conclude that 1) novel cross talk occurs between tumor necrosis factor receptor and TGF/epidermal growth factor receptor in stimulating MSC HGF production; 2) this cross talk is mediated, at least partially, via activation of MEK, p38, and PI-3K; 3) TGFstimulates MSCs to produce HGF by MEK, p38, PI-3K, and TNFR2-dependent mechanisms; and 4) TNFR1 acts to decrease basal TGFand TNF-stimulated HGF.
Oral exposure to inorganic arsenic: evaluation of its carcinogenic and non-carcinogenic effects

Inorganic arsenic, which is extensively metabolised in humans into even more toxic methylated arsenicals, is a potent carcinogen, causing tumours of the skin, lung, urinary bladder, and other organs. It also induces a number of non-cancer effects. Consumption of drinking water highly contaminated by arsenic causes serious health problems in some countries in southeastern Asia, and arsenic poses problems for drinking-water safety worldwide. Existing risk assessments are based on epidemiological studies from regions with high exposure concentrations (in the mg/L range). It is a matter of debate whether these findings are useful at predicting arsenic-induced effects at low concentrations. In recent years numerous epidemiological studies on cancer and non-cancer effects of inorganic arsenic have been published. This work aims at reviewing recent toxicological and epidemiological data on inorganic arsenic with emphasis on effects at low exposure concentrations. Information obtained from epidemiological studies is supplemented with mechanistic data from in vitro and in vivo studies. Various modes of action for arsenic carcinogenicity are discussed. The information gathered was used to evaluate the reliability of existing cancer-risk assessments and to improve current assessments of non-cancer health effects. A tolerable daily dose, based on epidemiological studies on arsenic-induced skin disorders, is presented.
CpG methylation plays a vital role in determining tissue- and cell-specific expression of the human cell-death-inducing DFF45-like effector A gene through the regulation of Sp1/Sp3 binding

Cell-death-inducing DFF45-like effector A (CIDE-A) belongs to a family of proapoptotic proteins, the expression of which is highly restricted in human tissues and cells. Here, the core region of the human CIDE-A promoter was characterized. Surprisingly, two Sp1/Sp3-binding sites, rather than tissue-specific transcription factors, were found to be required for the promoter activity. Although the ubiquitously expressed Sp1 and Sp3 were crucial, they alone could not adequately regulate the specific expression of CIDE-A. We found that the expression of CIDE-A was further regulated by CpG methylation of the promoter region. By performing bisulfite sequencing, we observed dense CpG methylation of the promoter region in tissues and cells with low or no expression of CIDE-A but not in tissues with high level of CIDE-A expression. In vitro methylation of this region showed significantly reduced transcriptional activity. Treatment of CIDE-A-negative cells with 5-aza-2′-deoxycytidine demethylated the CpG sites; this opened the closed chromatin conformation and markedly enhanced the binding affinity of Sp1/Sp3 to the promoter in vivo, thereby restoring CIDE-A expression. These data indicated that CpG methylation plays a crucial role in establishing and maintaining tissue- and cell-specific transcription of the CIDE-A gene through the regulation of Sp1/Sp3 binding.
TIED, LibsafePlus: Tools for Runtime Buffer Overflow Protection

Buffer overflow exploits make use of the treatment of strings in C as character arrays rather than as first-class objects. Manipulation of arrays as pointers and primitive pointer arithmetic make it possible for a program to access memory locations which it is not supposed to access. There have been many efforts in the past to overcome this vulnerability by performing array bounds checking in C. Most of these solutions are either inadequate, inefficient or incompatible with legacy code. In this paper, we present an efficient and transparent runtime approach for protection against all known forms of buffer overflow attacks. Our solution consists of two tools: TIED (Type Information Extractor and Depositor) and LibsafePlus. TIED extracts size information of all global and automatic buffers defined in the program from the debugging information produced by the compiler and inserts it back in the program binary as a data structure available at runtime. LibsafePlus is a dynamic library which provides wrapper functions for unsafe C library functions such as strcpy. These wrapper functions check the source and target buffer sizes using the information made available by TIED and perform the requested operation only when it is safe to do so. For dynamically allocated buffers, the sizes and starting addresses are recorded at runtime. With our simple design we are able to protect most applications with a performance overhead of less than 10%.
A Novel, Single Algorithm Approach to Predict Acenocoumarol Dose Based on CYP2C9 and VKORC1 Allele Variants

The identification of CYP2C9 and VKORC1 genes has strongly stimulated the research on pharmacogenetics of coumarins in the last decade. We assessed the combined influence of CYP2C9 *2 and *3, and VKORC1 c. -1639G>A, 497C>G, and 1173C>T variants, on acenocoumarol dosage using a novel algorithm approach, in 193 outpatients who had achieved stable anticoagulation. We constructed an “acenocoumarol-dose genotype score” (AGS, maximum score = 100) based on the number of alleles associated with higher acenocoumarol dosage carried by each subject for each polymorphism. The mean AGS was higher in the high-dose (>28mg/week) compared with the low-dose (<7mg/week) group (mean(SEM) of 84.1±3.4 vs. 62.2±4.8, P = 0.008). An AGS>70 was associated with an increased odds ratio (OR) of requiring high acenocoumarol dosage (OR: 3.347; 95%CI: 1.112–10.075; P = 0.032). In summary, although more research is necessary in other patient cohorts, and this algorithm should be replicated in an independent sample, our data suggest that the AGS algorithm could be used to help discriminating patients requiring high acenocoumarol doses to achieve stable anti-coagulation.
Intraoperative sonography during open partial nephrectomy for renal cell cancer: does it alter surgical management?

OBJECTIVE The purpose of this study is to evaluate whether intraoperative ultrasound (IOUS) during open partial nephrectomy alters the surgical management for renal cell cancer (RCC). MATERIALS AND METHODS One hundred ninety-eight consecutive patients undergoing IOUS during open partial nephrectomy for RCC were selected for retrospective review of clinical and imaging data. Patient age and sex, the local extent of the primary lesion, and the presence of additional lesions were recorded. Ultrasound findings were compared with preoperative CT or MRI to determine whether the IOUS findings changed surgical management. Summary statistics were performed to assess what percentage of patients with additional IOUS findings had a change in their surgical management. The Kaplan-Meier method was used to estimate 5-year overall survival (OS) and event-free survival (EFS) rates for all patients. Patients were followed for 9-12 years to assess survival and measure recurrence rates. RESULTS Twenty-one of 198 patients (10.6%; 95% CI, 6.7-15.8%) had additional findings on IOUS not seen on preoperative imaging. As a result, surgery was modified in 15 of these 21 patients (71.4%; 95% CI, 47.8-88.7%). The 5-year OS rate was 81%, and the EFS rate was 76% for the whole group; most deaths were due to unrelated causes. There was no statistically significant difference in OS (p = 0.867) and EFS (p = 0.069) rates among patients who had a change of management because of additional lesions seen by IOUS. CONCLUSION IOUS performed during open partial nephrectomy for resection of RCC shows additional findings compared with preoperative cross-sectional imaging that may alter surgical management.
Stable Isotope Probing Analysis of Interactions between Ammonia Oxidizers

ABSTRACT The response of natural microbial communities to environmental change can be assessed by determining DNA- or RNA-targeted changes in relative abundance of 16S rRNA gene sequences by using fingerprinting techniques such as denaturing gradient gel electrophoresis (DNA-DGGE and RNA-DGGE, respectively) or by stable isotope probing (SIP) of 16S rRNA genes following incubation with a 13C-labeled substrate (DNA-SIP-DGGE). The sensitivities of these three approaches were compared during batch growth of communities containing two or three Nitrosospira pure or enriched cultures with different tolerances to a high ammonia concentration. Cultures were supplied with low, intermediate, or high initial ammonia concentrations and with 13C-labeled carbon dioxide. DNA-SIP-DGGE provided the most direct evidence for growth and was the most sensitive, with changes in DGGE profiles evident before changes in DNA- and RNA-DGGE profiles and before detectable increases in nitrite and nitrate production. RNA-DGGE provided intermediate sensitivity. In addition, the three molecular methods were used to follow growth of individual strains within communities. In general, changes in relative activities of individual strains within communities could be predicted from monoculture growth characteristics. Ammonia-tolerant Nitrosospira cluster 3b strains dominated mixed communities at all ammonia concentrations, and ammonia-sensitive strains were outcompeted at an intermediate ammonia concentration. However, coexistence of ammonia-tolerant and ammonia-sensitive strains occurred at the lowest ammonia concentration, and, under some conditions, strains inhibited at high ammonia in monoculture were active at high ammonia in mixed cultures, where they coexisted with ammonia-tolerant strains. The results therefore demonstrate the sensitivity of SIP for detection of activity of organisms with relatively low yield and low activity and its ability to follow changes in the structure of interacting microbial communities.
Relative contributions of plantar fascia and ligaments on the arch static stability: a finite element study

Abstract The plantar fascia (PF) and major ligaments play important roles in keeping the static foot arch structure. Their functions and relative contributions to the arch stability have not been well studied. A three-dimensional finite element foot model was created based on the reconstruction of magnetic resonance images. During balanced standing, four cases after individual releases of the PF, spring ligament (SL), and long and short plantar ligaments (LPL and SPL) were simulated, to compare their biomechanical consequences with the normal predictions under the intact structure. Although the predictions showed the arch did not collapse obviously after each structure sectioning, the internal mechanical behaviors changed considerably. The PF release resulted in the maximal increases of approximately 91%, 65% and 47% in the tensions of the LPF, SPL and SL, produced the largest changes in all bone rotations, and brought an obvious shift of high stress from the medial metatarsals to the lateral metatarsals. The SL release mainly enhanced bone rotation angles and weakened the joint stability of the arch structure. The LPL and the SPL performed the roles of mutual compensation as either one was released. The influence of the LPL on the load distribution among metatarsals was greater than for the SPL and the SL.
Long-term outcomes with concurrent carboplatin, paclitaxel and radiation therapy for locally advanced, inoperable head and neck cancer.

BACKGROUND Our goal was to evaluate long-term efficacy outcomes of patients with squamous cell carcinoma of the head and neck (SCCHN) treated with carboplatin, paclitaxel (Taxol) and radiotherapy. PATIENTS AND METHODS We conducted a phase II trial in inoperable patients with locally advanced SCCHN. Carboplatin 100 mg/m(2) and paclitaxel 40 mg/m(2) were administered i.v. once a week during external beam radiation therapy (180 cGy per fraction) for 6-7 weeks. Interstitial brachytherapy was used as a boost in selected patients with primary malignancies of the oral cavity and the oropharynx. RESULTS Fifty-five patients were enrolled. Fifty-two patients (95%) had stage IV and 51 (93%) had technically unresectable disease; 62% had an oropharyngeal primary site. Twenty-one patients underwent brachytherapy boost. Grade 3 or 4 mucositis occurred in 30% of patients. One death occurred during treatment that was related to complications of gastrostomy tube placement. Forty of 50 assessable patients (80%) had an objective response, with a complete response rate of 52%. With a median follow-up of 69 months for surviving patients, the 5-year progression-free survival was 36% and the 5-year overall survival was 35%. Two of the 18 long-term survivors of >50 months were gastrostomy tube feeding dependent. Patients undergoing brachytherapy boost (n = 21) had similar outcomes compared with the rest of the patients. In multivariate analysis, baseline hemoglobin levels and N stage were predictive of survival. CONCLUSION Treatment with concurrent carboplatin, paclitaxel and radiation is safe and offers curative potential for poor prognosis patients with locally advanced SCCHN.
Kin selection, quorum sensing and virulence in pathogenic bacteria

Bacterial growth and virulence often depends upon the cooperative release of extracellular factors excreted in response to quorum sensing (QS). We carried out an in vivo selection experiment in mice to examine how QS evolves in response to variation in relatedness (strain diversity), and the consequences for virulence. We started our experiment with two bacterial strains: a wild-type that both produces and responds to QS signal molecules, and a lasR (signal-blind) mutant that does not release extracellular factors in response to signal. We found that: (i) QS leads to greater growth within hosts; (ii) high relatedness favours the QS wild-type; and (iii) low relatedness favours the lasR mutant. Relatedness matters in our experiment because, at relatively low relatedness, the lasR mutant is able to exploit the extracellular factors produced by the cells that respond to QS, and hence increase in frequency. Furthermore, our results suggest that because a higher relatedness favours cooperative QS, and hence leads to higher growth, this will also lead to a higher virulence, giving a relationship between relatedness and virulence that is in the opposite direction to that usually predicted by virulence theory.
Comparing Human and Machine Performance for Natural Language Information Extraction: Results from the Tipster Text Evaluation

This paper presents results from a study comparing human performance on the text of natural language information extraction with that of machine extraction systems that were developed as part of the ARPA Tipster program. Information extraction is shown to be a difficult task for both humans and machines. Evidence for one set of text material, English Microelectronics, indicated that a human analyst produces about half the errors as does machine systems.
Ribosomal Intergenic Spacer 1 Based Characterization of Button Mushroom (Agaricus bisporus) Strains

Abstract Breeding the button mushroom requires genetic information about its strains. This study was undertaken to genetically characterize four domestically bred button mushroom strains (Saea, Saejung, Saedo, Saeyeon cultivars) and to assess the possibility of using the intergenic spacer 1 (IGS1) region of rDNA as a genetically variable region in the genetic characterization. For the experiment, 34 strains of Agaricus bisporus, two strains of A. bitorquis, and one strain of A. silvaticus, from 17 countries were used. Nucleotide sequence analysis of IGS1 rDNA in these 37 Agaricus strains confirmed that genetic variations exist, not only among the four domestic strains, but also between the four domestic strains and foreign strains. Crossing two different haploid strains of A. bisporus seems to generate genetic variation in the IGS1 region in their off-spring haploid strains. Phylogenetic analysis based on the IGS1 sequence revealed all A. bisporus strains could be differentiated from A. silvaticus and A. bitorquis strains. Five genetic groups were resolved among A. bisporus strains. Saejung and Saeyeon cultivars formed a separate genetic group. Our results suggest that IGS1 could be complementarily applied in the polymorphism analysis of button mushroom.
Coaching Efficacy and Coaching Effectiveness: Examining Their Predictors and Comparing Coaches’ and Athletes’ Reports

Research on the conceptual model of coaching efficacy (Feltz, Chase, Moritz, & Sullivan, 1999) has increased dramatically over the past few years. Utilizing this model as the guiding framework, the current study examined: (a) coaching experience and sex as predictors of coaches’ coaching efficacy; (b) sport experience, sex, and the match/mismatch in sex between coach and athlete as predictors of athletes’ perceptions of their coach’s effectiveness on the four coaching efficacy domains; and (c) whether coaches’ reports of coaching efficacy and athletes’ perceptions of coaching effectiveness differed. Coaches (N = 26) and their athletes (N = 291) from 8 individual and 7 team sports drawn from British university teams (N = 26) participated in the study. Coaches completed the Coaching Efficacy Scale (CES), while athletes evaluated their coach’s effectiveness using an adapted version of the CES; coaches and athletes also responded to demographic questions. Results indicated that, in coaches, years of coaching experience positively predicted technique coaching efficacy, and males reported higher game strategy efficacy than females. In athletes, sport experience negatively predicted all perceived coaching effectiveness dimensions, and the mismatch in sex between athletes and their coach negatively predicted perceived motivation and character building coaching effectiveness. Finally, on average, coaches’ ratings of coaching efficacy were significantly higher than their athletes’ ratings of coaching effectiveness on all dimensions. The findings are discussed in terms of their implications for coaching effectiveness. Coaches are considered influential individuals in athletes’ lives. Coaches can positively affect athletes’ performance, behavior, and psychological and emotional well being (see Horn, 2002). The main medium through which coaches exert their influence on sport participants is their own behaviors, and coaches who have a positive impact on athletes engage in effective behaviors. Effective coaching behaviors are those that result in successful performance and positive psychological
The Use of Phosphatidylcholine for Correction of Lower Lid Bulging Due to Prominent Fat Pads

BACKGROUND Patients with prominent periorbital fat pads often complain of having a persistent “tired” look and seek treatment from their dermatologist. OBJECTIVE A non-surgical treatment of fat pads. METHODS Thirty patients were treated for prominent lower eyelid fat pads with phosphatidylcholine injection. Pre- and posttreatment photographs were taken for long-term analysis. RESULTS A marked reduction of the lower eyelid fat pads was noted over the 2-year follow-up period. There were no recurrences. CONCLUSION The injection of phosphatidylcholine (250 mg/5 ml) into the fat pads is a simple office procedure that may postpone or even substitute for lower eyelid blepharoplasty.
Benchmarking Streaming Computation Engines: Storm, Flink and Spark Streaming

Streaming data processing has been gaining attention due to its application into a wide range of scenarios. To serve the booming demands of streaming data processing, many computation engines have been developed. However, there is still a lack of real-world benchmarks that would be helpful when choosing the most appropriate platform for serving real-time streaming needs. In order to address this problem, we developed a streaming benchmark for three representative computation engines: Flink, Storm and Spark Streaming. Instead of testing speed-of-light event processing, we construct a full data pipeline using Kafka and Redis in order to more closely mimic the real-world production scenarios. Based on our experiments, we provide a performance comparison of the three data engines in terms of 99th percentile latency and throughput for various configurations.