Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription of germ line V alpha segments correlates with ongoing T-cell receptor alpha-chain rearrangement

M14T is a virally transformed immature T-cell line which continues to rearrange its T-cell antigen receptor (TCR) alpha-chain genes in vitro and thus represents a dynamic system for studying TCR assembly. In an effort to investigate whether the TCR alpha locus is accessible for V(D)J rearrangement events, we examined M14T cells for the presence of germ line TCR alpha transcripts. Several unrearranged V alpha segments were found to be transcriptionally active in M14T cells. By comparison, germ line V alpha transcripts are absent in nonlymphoid and pro-T-cell lines and barely detectable in mature T-cell lines, suggesting that this phenomenon is likely stage and tissue specific. We demonstrate a perfect correlation between transcriptionally active V alpha segments and their involvement in ongoing V alpha-to-J alpha rearrangements. In addition, data suggesting that the unrearranged J alpha locus is also transcriptionally active in the M14T line are presented. Furthermore, the recombination-activating genes RAG-1 and RAG-2 are differentially expressed, with RAG-2 detectable only by polymerase chain reaction, implying that very low levels of one of these gene products are sufficient to complement the other to facilitate VJ rearrangements. These findings provide the first direct evidence for an accessibility model of antigen receptor rearrangement in T cells.
Population size and stopover duration estimation using mark–resight data and Bayesian analysis of a superpopulation model

We present a novel formulation of a mark–recapture–resight model that allows estimation of population size, stopover duration, and arrival and departure schedules at migration areas. Estimation is based on encounter histories of uniquely marked individuals and relative counts of marked and unmarked animals. We use a Bayesian analysis of a state–space formulation of the Jolly–Seber mark–recapture model, integrated with a binomial model for counts of unmarked animals, to derive estimates of population size and arrival and departure probabilities. We also provide a novel estimator for stopover duration that is derived from the latent state variable representing the interim between arrival and departure in the state–space model. We conduct a simulation study of field sampling protocols to understand the impact of superpopulation size, proportion marked, and number of animals sampled on bias and precision of estimates. Simulation results indicate that relative bias of estimates of the proportion of the population with marks was low for all sampling scenarios and never exceeded 2%. Our approach does not require enumeration of all unmarked animals detected or direct knowledge of the number of marked animals in the population at the time of the study. This provides flexibility and potential application in a variety of sampling situations (e.g., migratory birds, breeding seabirds, sea turtles, fish, pinnipeds, etc.). Application of the methods is demonstrated with data from a study of migratory sandpipers.
The 'swoosh' test--an evaluation of a modified 'whoosh' test in children.

BACKGROUND Caudal analgesia is widely used in paediatric anaesthetic practice. In adults, the 'whoosh' test has been recommended as a guide to successful needle insertion, but it has not been extensively studied in paediatric patients. We have investigated a modification of the 'whoosh' test, which we have christened the 'swoosh' test. It avoids the injection of air by performing auscultation during injection of the local anaesthetic solution. We have compared it with clinical judgement of correct placement. METHODS We studied 113 children undergoing elective surgery. During insertion of the caudal block, a stethoscope was placed over the lower lumbar spine and the presence or absence of an audible 'swoosh' noted. The operator's clinical impression of successful insertion was also recorded. RESULTS The overall success rate of caudal anaesthesia was 95.6%. Of the 108 patients with a successful block, 98 had a positive 'swoosh' test. There were no false positive results. Calculations show the 'swoosh' test to have a sensitivity of 91%, a specificity of 100% and a positive predictive value of 100%. CONCLUSIONS The 'swoosh' test is a simple and accurate test to confirm successful caudal insertion in children, and is especially useful as a teaching aid for anaesthetists new to the technique.
The “Low Dose” Hypothesis: Validity and Implications for Human Risk

In the late 1990s, a “low dose” hypothesis was proposed based on studies that purported to show that hormonally active environmental agents were causing a variety of effects, mainly reproductive and developmental, at “low doses. ” The supporters of this hypothesis claim that traditional “high-dose” toxicity studies are not adequate to assess adverse effects from these hormonally active agents in that they do not detect effects that are occurring at “low doses. ” In addition, it is claimed that these “low dose” effects are occurring at levels comparable to those to which humans are being exposed. These claims have been controversial and expert panels evaluated the evidence behind them in the early 2000s. Although these panels generally concluded that such “low dose” effects were not conclusively established, proponents of the “low dose” hypothesis assert that a large number of more recent studies now provide clear support for their hypothesis. This review carefully examines both recent and older studies that have been cited to support the “low dose” hypothesis, including their relevance for the human population. These include in vivo and in vitro laboratory studies as well as a very limited number of epidemiological investigations. Based on the evidence, it is concluded that these “low dose” effects have yet to be established, that the studies purported to support these cannot be validly extrapolated to humans, and the doses at which the studies have been performed are significantly higher than the levels to which humans are exposed.
Retinal optical coherence tomography: past, present and future perspectives

Optical coherence tomography (OCT) has undergone substantial changes since its first use in the 1990s. Although the first generation of OCT systems heralded a new era in the non-invasive diagnostic options in ophthalmology, they did not reveal much detail. Later devices offered more information and helped in the diagnosis and treatment of a variety of pathological conditions, primarily of the retina. With today's spectral-domain type models ophthalmologists are offered a comprehensive tool with the opportunity for early diagnosis and precise monitoring of patients with retinal and glaucomatous pathologies. However, as experience with these new devices grows and demands by clinicians and researchers rise, further improvements need to be addressed. Future developments in the improvement of the transverse resolution and extension of the penetration depth are to be expected. New modalities such as polarisation sensitive OCT (PS-OCT) or Doppler OCT are now in use and promise additional insights in the properties of physiological and pathological tissue. While PS-OCT reveals further detail in alterations of the retinal pigment epithelium, Doppler OCT gives additional information about blood flow measurements. With these and further new developments, OCT will continue to be an invaluable instrument in the armamentarium of modern ophthalmology.
All-atom molecular dynamic simulations and relative NMR spectra study of weak C-H...O contacts in amide-water systems.

Amide-water mixtures are studied by all-atom molecular dynamics (MD) simulations and the relative temperature-dependent NMR experiment. The weak C-H.O contacts are found in the amide-water systems theoretically and experimentally. The statistical results of the average numbers of hydrogen bonds indicate that the methyl groups in amide molecules represent different capabilities in forming the weak C-H.O contacts. The statistics also imply that the C-H.O contacts are more obvious in the amide-rich region than those in the water-rich region. The temperature-dependent NMR spectra are also adopted to investigate the weak C-H.O contacts in the amide-water systems. The relative chemical shifts of the methyl groups are in good agreement with the MD simulations.
Anti-Müllerian hormone levels after laparoscopic cystectomy for endometriomas as a possible predictor for pregnancy in infertility treatments

Abstract We assessed the associations between preoperative and postoperative serum anti-Müllerian hormone (AMH) levels and parameters of endometriosis and endometriomas surgery with the success of infertility treatments after cystectomy. Seventeen out of 54 patients got pregnant during the infertility treatments. In these patients, the median interval from surgery to conception was 16.3 months. The serum AMH levels 1-year postoperatively were significantly higher in the pregnant group compared to the non-pregnant group (3.44 ± 1.78 versus 2.17 ± 2.24 ng/ml, p = 0.049). The median interval from surgery to recurrence was 34.4 months, and no significant differences were found in the serum AMH levels at any time point between the recurrence and non-recurrence groups. Serum AMH levels 1 year after laparoscopic cystectomy for endometriomas may predict the success of postoperative infertility treatments, but not a recurrence of endometriomas.
Wheel: Accelerating CNNs with Distributed GPUs via Hybrid Parallelism and Alternate Strategy

Convolutional Neural Networks (CNNs) have been widely used and achieve amazing performance, typically at the cost of very expensive computation. Some methods accelerate the CNN training by distributed GPUs those deploying GPUs on multiple servers. Unfortunately, they need to transmit a large amount of data among servers, which leads to long data transmitting time and long GPU idle time. Towards this end, we propose a novel hybrid parallelism architecture named "Wheel" to accelerate the CNN training by reducing the transmitted data and fully using GPUs simultaneously. Specifically, Wheel first partitions the layers of a CNN into two kinds of modules: convolutional module and fully-connected module, and deploys them following the proposed hybrid parallelism. In this way, Wheel transmits only a few parameters of CNNs among different servers, and transmits most of the parameters within the same server. The time to transmit data is significantly reduced. Second, to fully run each GPU and reduce the idle time, Wheel devises an alternate strategy deploying multiple workers on each GPU. Once one worker is suspended for receiving data, another one in the same GPU starts to execute the computing task. The workers in each GPU run concurrently and repeatedly like Wheels. Experiments are conducted to show the outperformance of the proposed scheme over the state-of-the-art parallel approaches.
An Improved Identity-Based KCDSA Signcryption Scheme

KCDSA (Korean Certificate-based Digital Signature Al- gorithm) is the Korean digital signature standard. In 2006, Ryu, Jeong, and Seo proposed three identity-based sign- cryption schemes based on KCDSA. However, their schemes provide either public verifiability or forward security. That is, the properties of public verifiability and forward secu- rity are mutually exclusive in their schemes. In this paper, we propose an improved scheme that provides both public verifiability and forward security. We give a formal proof of semantic security under the Decisional Bilinear Diffie- Hellman assumption for this improved scheme in the ran- dom oracle model.
Situational analysis of the type and degree of resorption of the interdental septum of teeth with approximal amalgam restorations.

AIM The aim of the study was to determine radiographically the type and degree of resorption of the interdental septum of teeth with approximal amalgam restorations in various iatrogenic clinical situations. METHODS Situational analysis of the type and degree of resorption of the interdental septum was performed in 757 approximal amalgam restorations of Class II cavities (according to Black). Intraoral periapical retroalveolar radiographs were used for that purpose. The condition of the septum was investigated in restorations with correct shape, in restorations with a poorly restored anatomical form, unsatisfactory marginal adaptation, as well in restorations with no proximal contact with the adjacent tooth. RESULTS The horizontal type of interdental septum resorption was the predominant type in all study groups. Restorations with poor anatomical form showed considerably higher incidence of vertical type of resorption in comparison with correctly shaped fillings. Similarly, restorations with unsatisfactory marginal adaptation demonstrated higher incidence of the disproportionate type of resorption than in the accurately formed group. A greater degree of resorption of the interdental septum was observed in restorations with incorrect anatomical form, with unsatisfactory marginal adaptation and with no contact with the adjacent tooth. CONCLUSION The observed changes can be explained by the presence of significant, long-standing retention of bacterial plaque, as well as by the additional trauma caused while eating and maintaining personal oral hygiene.
Comparison of Polymerase Chain Reaction and the Indirect Particle Agglutination Antibody Test for the Diagnosis of Mycoplasma pneumoniae Pneumonia in Children During Two Outbreaks

Background: Diagnosis of Mycoplasma pneumoniae pneumonia is challenging because of the lack of standardized rapid tests. Many serologic tests and polymerase chain reaction (PCR) based methods are used with different diagnostic criteria. Methods: This retrospective study was conducted to compare the diagnostic values of the indirect particle agglutination test and nested PCR of nasopharyngeal aspirates for the diagnosis of M. pneumoniae pneumonia in children. These assays were evaluated in 234 hospitalized children with community-acquired lower respiratory tract infections during 2 outbreaks of M. pneumoniae pneumonia in 2000 and 2003. Results: The cumulative PCR positive rate was 26.7% in patients with maximum antibody titers of ≤1:320 and 78.2% in those with titers of ≥1:640. Based on these data, a positive PCR, a 4-fold increase in antibody titer, or a single titer ≥1:640 were considered to indicate acute M. pneumoniae infection. Overall, 152 children were diagnosed to have M. pneumoniae pneumonia; 27 (18%) by serology only, 26 (17%) by PCR only, and 99 (65%) by both methods. Children who were diagnosed by PCR only were significantly younger (P = 0.003) and were more often immunocompromised (P = 0.019) than those that were PCR negative. Duration of cough before PCR diagnosis was shorter in cases diagnosed by PCR only than those that were PCR negative (P = 0.045). Conclusions: In conclusion, during the 2 outbreaks of M. pneumoniae infection, we found that the PCR test may be useful for the rapid diagnosis of M. pneumoniae pneumonia, particularly in young children and in immunocompromised patients and in early stage disease.
The Role of Mast Cells in the Development of 2, 4, 6-Trinitrobenzene Sulfonic Acid-Induced Colitis in Rats

Background: The role of mast cells in Crohn disease (CD) remains to be established. The aim of this study was to elucidate this in the development of CD-like colitis in rats by the use of mast-cell-deficient Ws/Ws and their control W+/W+ rats. Methods: CD-like colitis was induced in both groups by an enema of 10 mg of 2, 4, 6-trinitrobenzene sulfonic acid (TNBS) in 50% ethanol. Colonic damage, adhesion and colonic weight were measured at 7 and 14 days after the TNBS/ethanol enema. Rat mast cell protease-2 (RMCP-2) in the colonic tissue was also measured at 7 days after the enema. Results: There was no significant difference between W+/W+ and Ws/Ws rats in terms of colonic damage, adhesion or colonic weight. The tissue content of RMCP-2 in Ws/Ws rats treated with either saline or TNBS/ethanol was only maintained at a much lower level than that in W+/W+ rats with the corresponding treatment. Conclusions: These results demonstrate that mast cells are not essential in the development of 2, 4, 6-trinitrobenzene sulfonic acid-induced colitis in rats.
Activation and inactivation of cancer chemotherapeutic agents by rat hepatocytes cocultured with human tumor cell lines.

While colony formation assays provide sensitive indices of tumor cell proliferation and growth inhibition imposed by many chemotherapeutic agents, drugs which require metabolic activation lack activity in such assays. In the present study, we have utilized freshly isolated rat hepatocytes for the activation of drugs which are metabolized by hepatic microsomal as well as extra-microsomal enzymes. Hepatocytes in fluid medium are placed over soft-agarose matrix containing tumor-derived cells (e.g., A204, A549) within 35-mm culture dishes; drug and/or drug vehicle is added directly to the hepatocyte layer, and cultures are incubated for 24 hr prior to removal of the hepatocyte layer. Tumor cell colony formation is assessed following 7 to 10 days of incubation. Cyclophosphamide was used as a prototype agent to assess utility of the coculture methodology. In vivo treatment of rats with phenobarbital prior to hepatocyte isolation enhances cyclophosphamide toxicity in vitro, whereas pretreatment with carbon tetrachloride markedly reduced subsequent in vitro cyclophosphamide cytotoxicity. Hepatocyte:tumor cell cocultures provide an efficient means to detect metabolic activation and inactivation of several selected cancer chemotherapeutic agents as well. In the presence of hepatocytes, the 50% growth-inhibitory concentrations for cyclophosphamide, indicine N-oxide, and procarbazine are markedly decreased, whereas the 50% growth-inhibitory concentrations for [2,5-bis(1-aziridinyl)-3,6-diazo-1,4-cyclohexadiene-1,4-diyl]bis(c arbamic acid)diethyl ester, 1,3-bis-chloro(2-chloroethyl)-1-nitrosourea, dacarbazine, 5-fluorouracil, ftorafur, 1-(2-chloroethyl)-3-(4-methylcyclohexyl)-1-nitrosourea, and vincristine are significantly increased. By contrast, the 50% growth-inhibitory concentrations for actinomycin D, mitomycin C, 6-mercaptopurine, and other agents are unaffected by hepatocyte presence. Cryopreserved hepatocytes exhibit detectable levels of drug activation, although inadequate for routine use. Results suggest that hepatocyte:tumor cell cocultures may be well-suited for assessing the degree to which hepatic metabolism may activate or inactivate new anticancer drugs.
CFO Narcissism and Financial Reporting Quality

We investigate the effect of CFO narcissism, as measured by signature size, on financial reporting quality. Experimentally, we validate that narcissism predicts misreporting behavior, and that signature size predicts misreporting through its association with narcissism. Empirically, we examine notarized CFO signatures and find CFO narcissism is associated with more earnings management, less timely loss recognition, weaker internal control quality, and a higher probability of restatements. The results are consistent for within-firm comparisons focusing on CFO changes and are robust to controlling for CFO overconfidence and CEO narcissism. The results highlight the importance of CFO characteristics in the domain of financial reporting decisions.
Combination of positioning therapy and venovenous extracorporeal membrane oxygenation in ARDS patients

Positioning therapy may improve lung recruitment and oxygenation and is part of the standard care in severe acute respiratory distress syndrome (ARDS). Venovenous extracorporeal membrane oxygenation (vvECMO) is a rescue strategy that may ensure sufficient gas exchange in ARDS patients failing conventional therapy. The aim of this case series was to describe the feasibility and pitfalls of combining positioning therapy and vvECMO in patients with severe ARDS. A retrospective cohort of nine patients is described. The patients received 20 (15–86) hours (median, 25th and 75th percentile) of positioning therapy while being treated with vvECMO. The initial PaO2/FiO2 index was 64 (51–67) mmHg and the arterial carbon dioxide tension was 60 (50–71) mmHg. Positioning therapy included 135 degrees prone, prone positioning and continuous lateral rotational therapy. During the first three days, the oxygenation index improved from 47 (41–47) to 12 (11–14) cmH2O/mmHg. The lung compliance improved from 20 (17–28) to 42 (27–43) ml/cmH2O. Complications related to positioning therapy were facial oedema (n=9); complications related to vvECMO were entrance of air (n=1) and pump failure (n=1). However, investigation of root causes revealed no association with the positioning therapy and had no documented effect on the outcome. The reported cases suggest that positioning therapy can be performed safely in ARDS patients treated with vvECMO, providing appropriate precautions are in place and a very experienced team is present.
Performance analysis of SNMP in airborne tactical networks

SNMP, SNMPv2 and SNMPv3 are the standard protocols for network management in traditional wired networks. New RFCs have updated SNMP, but it remains focused on high-availability, high-bandwidth networks. In the dynamic MANET of tactical edge networks, fast-moving aircraft and terrain obscuration combine to create conditions where traditional SNMP is less effective. In this paper, we propose innovative ways to improve SNMP agent/manager interactions, specifically addressing the limitations of a bandwidth constrained tactical edge network. We will analyze the performance improvements using a variety of aggregation techniques of multicast, reliable multicast and aggregation techniques to enhance the SNMP agent/manager interactions thus conserving bandwidth but still monitor and provide network situational awareness to the war fighter. Performance analysis will be conducted through a combination of simulation and emulation environments, and the results will be discussed.
Correlation between coastal tides and the speed of commercial vessels

One way of saving fuel is to take advantage of the currents. This study investigates how the SOG of individual vessels in the Oslo Fjord is linked to current strength. The Oslo Fjord is approximately 150 km long; the areas of interest are one inner part and one outer part. The majority of vessels operating in these areas are heading either north (inbound) or south (outbound). Vessel traffic statistics for a duration of two years were collected by using the Automatic Identification System (AIS) and combined with tidal current measurements. Passenger, cargo and cruise vessels are considered. One finding is that the average SOG is in general larger for the vessels heading south than north in the narrow, inner parts of the Oslo Fjord. While in the wider, outer parts the average SOG is independent of the heading. The change in SOG due to tidal currents are stronger for passenger ferries heading south in the outer part of the Oslo Fjord even though the tidal currents in the outer part of the fjord are weaker than in the inner parts of the fjord. One simple explanation might be that the vessels adjust their speed through water to compensate for the currents in the inner parts of the fjord, but fail to readjust when the currents decrease in the outer parts of the fjord. The SOG of the cargo and cruise vessels seems to be less influenced by the tidal currents. The results indicate that several vessels can benefit more from exploiting the tidal currents to a larger extent.