gebhart/patrepeval huggingface dataset:
S216 Automated Cecal Intubation Rate and Withdrawal Time With Artificial Intelligence. A Video Validation Study (2021)

Introduction: Artificial Intelligence (AI) is poised to positively impact patient care and clinical workflows. Beyond assisting polyp detection during colonoscopy, artificial intelligence (AI) has the potential to automatically record key quality measures during colonoscopy, including cecal intubation rate and withdrawal time. We previously developed and reported algorithms to detect first frames of insertion, cecum, and withdrawal. Here we report video validation of these algorithms. Methods: Ninety-six deidentified videos recorded as part of a multicenter randomized trial were utilized. The ground truth was established by video review, marking the times of insertion (gtIN), first clear view of cecum (gtCEC), and withdrawal from the colon (gtOUT), relative to the first frame of the video. Ground truth withdrawal time (gtWT) was calculated by subtracting gtCEC from gtOUT. A secondary comparator included withdrawal times manually recorded by study coordinators in the AIDA trial (manWT). AI algorithms for IN, CECUM and OUT were subsequently run on all videos to record times of aiIN, aiCEC and aiOUT, respectively. We then compared withdrawal times between ground truth, manually entered and AI-predicted values (gtWT vs manWT vs aiWT). Results: Of the 96 videos reviewed, one did not reach cecum so gtWT could not be calculated. AI did not identify cecum in 2 videos, one of which was a true negative (cecum was not reached) and the other was a false negative. There was one false positive aiCEC identified 16 minutes before cecum was reached. Correlation between aiWT and gtWT was excellent (Figure 1A), and performed much better than manWT (Figure 1B). The mean difference between ground truth and ai-predicted withdrawal time (gtWT-aiWT) was 31 seconds, whereas the mean difference between gtWT and manWT is 130 seconds. This difference was statistically significant (p value of < 0.001). AI identified cecum with 98% sensitivity and specificity. Conclusion: This video validation study demonstrates the feasibility of automated and accurate recording of cecal intubation rate and withdrawal time using artificial intelligence. Its accuracy exceeds manual recording during colonoscopy by study coordinators.Figure 1.: A. (left panel) Comparison of ground truth (video review) withdrawal times (gtWT) vs AI-predicted withdrawal time (aiGT). The outlier represents a single false positive cecum identified by AI 16 minutes before cecum was actually reached. B. (right panel) - Comparison of ground truth video review withdrawal time (gtWT) vs manually entered withdrawal time by AIDA trial study coordinators (manWT).
SWISS‐2DPAGE: A database of two‐dimensional gel electrophoresis images (1993)

This publication presents the SWISS-2DPAGE database which gathers data on proteins identified on various two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) maps. Each SWISS-2DPAGE entry contains data on one protein, including mapping procedures, physiological and pathological data and bibliographical references, as well as several 2-D PAGE images showing the protein location. Links are also provided to other databases such as SWISS-PROT, EMBL, PROSITE and OMIM. The database has been set up on a server which may be accessed from any computer connected to the internet and it also makes it possible to display the theoretical location of proteins, the positions of which are not yet known on the 2-D PAGE.
Refining Network Alignment to Improve Matched Neighborhood Consistency (2021)

Network alignment, or the task of finding meaningful node correspondences between nodes in dierent graphs, is an important graph mining task with many scientific and industrial applications. An important principle for network alignment is matched neighborhood consistency (MNC): nodes that are close in one graph should be matched to nodes that are close in the other graph. We theoretically demonstrate a close relationship between MNC and alignment accuracy. As many existing network alignment methods struggle to preserve topological consistency in di cult scenarios, we show how to refine their solutions by improving their MNC. Our refinement method, RefiNA, is straightforward to implement, admits scalable sparse approximation, and can be paired post hoc with any network alignment method. Extensive experiments show that RefiNA increases the accuracy of diverse unsupervised network alignment methods by up to 90%, making them robust enough to align graphs that are 5 more topologically dierent than were considered in prior work.
[Reduction of patient discomfort, risks and costs, but not pregnancies, by a mild strategy for in-vitro fertilisation]. (2008)

After 1 year of treatment, the cumulative percentage of pregnancies leading to full-term live birth and the total patient discomfort were the same for the mild treatment (average 2.3 IVF-cycles) and the standard treatment (average 1.7 IVF-cycles). The mild treatment significantly reduced the number of multiple pregnancies and the overall costs.
Opportunities and challenges of static code analysis of IEC 61131-3 programs (2012)

Static code analysis techniques analyze programs by examining the source code without actually executing them. The main benefits lie in improving software quality by detecting potential defects and problematic code constructs in early development stages. Today, static code analysis is widely used and numerous tools are available for established programming languages like C/C++, Java, C# and others. However, in the domain of PLC programming, static code analysis tools are still rare. In this paper we present an approach and tool support for static code analysis of PLC programs. The paper discusses opportunities static code analysis can offer for PLC programming, it reviews techniques for static analysis, and it describes our tool that implements a rule-based analysis approach for IEC 61131-3 programs.
Tolerant compressed sensing with partially coherent sensing matrices (2017)

Most of compressed sensing (CS) theory to date is focused on incoherent sensing, that is, columns from the sensing matrix are highly uncorrelated. However, sensing systems with naturally occurring correlations arise in many applications, such as signal detection, motion detection and radar. Moreover, in these applications it is often not necessary to know the support of the signal exactly, but instead small errors in the support and signal are tolerable. Despite the abundance of work utilizing incoherent sensing matrices, for this type of tolerant recovery we suggest that coherence is actually beneficial . We promote the use of coherent sampling when tolerant support recovery is acceptable, and demonstrate its advantages empirically. In addition, we provide a first step towards theoretical analysis by considering a specific reconstruction method for selected signal classes.
Liver repopulation with xenogenic hepatocytes in B and T cell-deficient mice leads to chronic hepadnavirus infection and clonal growth of hepatocellular carcinoma (1998)

To investigate host and viral mechanisms determining hepadnaviral persistence and hepatocarcinogenesis, we developed a mouse model by transplanting woodchuck hepatocytes into the liver of mice that contain the urokinase-type plasminogen activator transgene (uPA) and lack mature B and T lymphocytes due to a recombination activation gene 2 (RAG-2) gene knockout. The woodchuck hepatocytes were transplanted via intrasplenic injection and were found to integrate into the recipient mouse liver cord structure. Normal adult woodchuck hepatocytes proliferated and reconstituted up to 90% of the uPA/RAG-2 mouse liver. uPA/RAG-2 mice containing woodchuck hepatocytes were infectable with woodchuck hepatitis virus (WHV) and showed WHV replication for at least 10 months with titers up to 1 x 10(11) virions per ml in the peripheral blood. WHV-infected hepatocytes from chronic carrier woodchucks also established a persistent infection in uPA/RAG-2 mice after an 8- to 12-week lag period of viremia. Although WHV envelope, core, and X proteins were produced in the uPA/RAG-2 mice, no inflammatory host immune response was observed in the liver of WHV-replicating mice. A first antiviral test demonstrated a greater than four orders of magnitude drop in WHV titer in response to interferon alpha treatment. WHV replication was up-regulated by dexamethasone treatment. Comparison of precancerous lesions in donor woodchucks versus recipient uPA/RAG-2 mice revealed an enrichment of dysplastic precancerous hepatocytes in transplanted mice. Clonal amplification of hepatocytes from a woodchuck with hepatocellular carcinomas was demonstrated by the detection of unique WHV DNA integration patterns in hepatocellular carcinomas that arose in uPA/RAG-2 mice. In the absence of B or T cell-mediated immune responses, WHV establishes a persistent noncytotoxic infection of woodchuck hepatocytes in uPA/RAG-2 chimeric mouse livers. Further studies of the kinetics of hepadnavirus infection and replication in quiescent and proliferating hepatocytes should increase our understanding of hepadnavirus spread and aid in the design of therapies to block or cure persistent infection.
Patterns of Helicobacter pylori isolate resistance to fluoroquinolones, amoxicillin, clarithromycin and metronidazoles. (2006)

Helicobacter pylori eradication using the three antibiotic regimen of amoxicillin, clarithromycin and metronidazole often fails, making it imperative to find substitutes. The following study made use of 72 H. pylori isolates derived from pyloric antrum mucosa biopsies of gastritis and chronic dyspepsia patients treated at the Cipto Mangunkusumo National General Hospital and three private hospitals in Jakarta. Testing for H. pylori sensitivity to various antimicrobials was conducted using the disk diffusion method (Kirby Bauer) and procedures determined by the Clinical and Laboratory Standards Intitute (CLSI)/NCCLS. The resistance rates of the isolates were 100% for metronodazole, 27.8% for clarithromycin, 19.4% for amoxicillin, 6.9% for ciprofloxacin, norfloxacin and ofloxacin, 2.8% for sparfloxacin and gatifloxacin, and 1.4% for levofloxacin and moxifloxacin. Fluoroquinolons have the lowest resistance compared to amoxicillin, clarithromycin and metronidazole.
U. S. Foreign policy in the 1956 Suez crisis (1971)

This thesis has dealt critically with U. S. diplomacy during the 1956 Suez crisis. The American approach was correct in opposing the use of force by the allies, but was at times confusing to them. The main conclusion of this thesis is that such misunderstandings are inevitable in the complicated realm of International politics. The American response in 1956 represents a search for a viable American policy toward the Middle East. A study of these events also helps one to understand the present tension in that area of the world, a tension that is of crucial importance to international peace and security.
EMG-based prediction of shoulder and elbow kinematics in able-bodied and spinal cord injured individuals (2000)

We have evaluated the ability of a time-delayed artificial neural network (TDANN) to predict shoulder and elbow motions using only electromyographic (EMG) signals recorded from six shoulder and elbow muscles as inputs, both in able-bodied subjects and in subjects with tetraplegia arising from C5 spinal cord injury. For able-bodied subjects, all four joint angles (elbow flexion-extension and shoulder horizontal flexion-extension, elevation-depression, and internal-external rotation) were predicted with average root-mean-square (rms) errors of less than 20 degrees during movements of widely different complexities performed at different speeds and with different hand loads. The corresponding angular velocities and angular accelerations were predicted with even lower relative errors. For individuals with C5 tetraplegia, the absolute rms errors of the joint angles, velocities, and accelerations were actually smaller than for able-bodied subjects, but the relative errors were similar when the smaller movement ranges of the C5 subjects were taken into account. These results indicate that the EMG signals from shoulder and elbow muscles contain a significant amount of information about arm moVement kinematics that could be exploited to develop advanced control systems for augmenting or restoring shoulder and elbow movements to individuals with tetraplegia using functional neuromuscular stimulation of paralyzed muscles.
Is innate enough? The innate immune response in Drosophila (2004)

In recent years, the innate immune system has emerged from the shadow of adaptive immune responses as a major area of research in its own right. One of the most significant model systems that has been used to investigate this phenomenon has been the fruit fly, Drosophila melanogaster. Exploration of the differential immune response presented by Drosophila led to the discovery of important signalling events and transduction pathways, which were thereafter shown to be specific for the type of infecting pathogen. These factors and pathways were subsequently found to have homologues in many other organisms, including those with adaptive immune responses. In light of the present status of studies in innate immunity, this review describes the current state of understanding of the Drosophila immune response.
Novel modulation and detection for bandwidth-reduced RZ formats using duobinary-mode splitting in wideband PSK/ASK conversion (2002)

This paper proposes a novel duobinary-mode-splitting scheme that uses wideband phase-shift-keying (PSK)/amplitude-shift-keying (ASK) conversion for modulation and detection of bandwidth-reduced return-to-zero (RZ) modulation formats. We have first demonstrated that the proposed scheme greatly simplifies the modulation process of the duobinary carrier-suppressed RZ format (DCS-RZ) based on baseband binary nonreturn-to-zero (NRZ) modulation. We also proposed carrier-suppressed RZ differential-phase-shift-keying format (CS-RZ DPSK) as a novel bandwidth-reduced RZ format by applying the proposed scheme in the detection process. These novel RZ formats are shown to be very useful for dense wavelength-division multiplexed (DWDM) transport systems using high-speed channels, over 40 Gb/s, with spectrum efficiencies higher than 0.4 b/s/Hz. We demonstrate that the proposed modulation and detection scheme greatly simplifies the DWDM transmitter and receiver configuration if the periodicity of the optical PSK/ASK conversion filter equals the WDM channel spacing. The large tolerance of the formats against several fiber nonlinearities and their wide dispersion tolerance characteristics are tested at the channel rate of 43 Gb/s with 100-GHz spacing. The novel CS-RZ DPSK format offers higher nonlinearity tolerance against cross-phase modulation than does the DCS-RZ format.
"Thin" vs. "fat" visualization client (2002)

The paper explains the advantage of using low-cost, configurable, data visualization components, which can be embedded and distributed in electronic documents and reports. With the increasing use of electronic documents, distributed by intranets and the Internet, the opportunity to provide interactive visualization techniques within scientific and engineering reports has become practicable. This new technology of components allows authors of a report to distribute with a specific "data viewer", for example, allowing the recipients to interactively examine the data in the same way as the original analyst. A "thin" client, by definition, has minimal software requirements necessary to function as a user interface front-end for a Web enabled application and raises the issue of client vs. Server data visualization rendering. Real-time visual data manipulation doesn't translate well into a "thin" client. While the VRML file format allows distribution of 3D visualization scenes to the Web, the user has no direct access to the underlying data sources. The "mapping" of numerical data into geometry format (VRML) takes place at the server side. In the "thin" client model, nearly all functionality is delivered from the server side of the visualization engine while the client perform very simple display and querying functions.
Cyclosporin A: a powerful immunosuppressant. (1982)

Cyclosporin A (CyA) is a powerful immunosuppressive agent whose lack of myelotoxicity makes it unique among nonsteroidal drugs currently given for immunosuppression. It has been used with initial success in recipients of kidney, liver, bone marrow and pancreas transplants, and it may also have clinical application in the treatment of autoimmune disorders. In regard to its use in transplant recipients, there are many remaining questions about its mechanism of action, the optimum dose, whether it should be used alone or with other immunosuppressants, whether it can suppress chronic rejection and what its long-term side effects may be. These questions can only be answered by further careful laboratory investigation and controlled clinical trials. Until then, CyA should only be administered in centres experienced in its use.
Network Performance Criteria for Telecommunication Traffic Types driven by Quality of Experience (2019)

A common reason for changing the chosen service provider is the users' perception of service. Quality of Experience (QoE) describes the end user's perception of service while using it. A frequent cause of QoE degradation is inadequate traffic routing, where, other than throughput, selected routes do not satisfy minimum network requirements for the given service or services. In order to enable QoE-driven routing, per traffic type defined routing criteria are required. Our goal was to obtain those criteria for relevant services of a telecom operator. For the purpose of identifying services of interest, we first provide short results of user traffic analysis within the telecom operator network. Next, our work presents testbed measurements which explore the impact of packet loss and delay on user QoE for video, voice, and management traffic. For video services, we investigated separately multicast delivery, unicast HTTP Live Streaming (HLS), and unicast Real Time Streaming Protocol (RTSP) traffic. Applying a threshold to QoE values, from the measured dependencies we extracted minimum network performance criteria for the investigated different types of traffic. Finally, we provide a comparison with results available in the literature on the topic.
Timestamp nets in technical applications (2002)

Timestamp Petri nets, introduced in this paper, offer a new method to deal with time critical problems in the field of automation of manufacturing systems. To each token in a timestamp net a timestamp is assigned, which denotes the time when the token was put on its place. In those nets intervals are assigned to the incoming edges of transitions, which describe the permeability of the edge relative to the token on the adjacent place. In timestamp nets it is possible that synchronizing transitions are not able to fire although they are supplied with tokens sufficiently, because their incoming edges are not permeable simultaneously. In this case we say the transition got timewise stuck. In this paper it is examined how transitions of a timestamp net are getting timewise stuck. Based on a symbolic analysis, these investigations can be reduced to solving systems of linear inequalities. The method can also be used to determine parameters for a timestamp net in order to prevent transitions from getting timewise stuck. We show the method's applicability by the dynamic model of a small technical plant as an example. Forbidden states of the uncontrolled system are described by transitions which can get timewise stuck. We use the method to determine time parameters of a controller, which ensures that forbidden states in the controlled system are unreachable.
Climate-sargassum interactions across scales in the tropical Atlantic (2023)

The impacts of climate change on ecosystems are highly uncertain but potentially profound. One such impact may be the emergence of extensive mats of seaweed (macroalgae), due to the extraordinary proliferation of pelagic sargassum species, in the tropical Atlantic since 2011. Sargassum blooms are now an annual event and reached record levels across what is now known as the ‘Great Atlantic Sargassum Belt’ (GASB) in summer 2022. Monitoring across scales, from satellite surveillance to in-situ beach surveys, is bringing step changes in process-level understanding of sargassum. Physical and biogeochemical drivers of sargassum act at basin scale to shape the GASB, highly variable from year to year. In the local environment, sargassum is sensitive to ambient conditions, with new findings confirming that growth rates are temperature dependent. Multidecadal ocean warming may therefore be detrimental to sargassum, although projected changes in other drivers are uncertain. Emerging options for climate change action around sargassum include valorisation and carbon sequestration, although uncertainties are again considerable. In conclusion, the emergence of sargassum across the tropical Atlantic highlights interconnected systems that embrace physical, biogeochemical, and socioeconomic dimensions, with considerable scope for improved monitoring, process-level understanding and prediction.
Secondary zoonotic dog-to-human transmission of SARS-CoV-2 suggested by timeline but refuted by viral genome sequencing (2022)

The results of this case support current knowledge about the low risk of secondary zoonotic dog-to-human transmissions of SARS-CoV-2 and emphasizes the strength of genomic sequencing in deciphering viral transmission chains.
Salvage brachytherapy for prostate bed recurrence following radical prostatectomy. (2013)

218 Background: Approximately 10% of patients who undergo a radical prostatectomy (RP) for localized prostate cancer subsequently experience a local recurrence. A small percentage of these patients present with prostate bed nodules (PBN). We present here, a case series of 12 patients treated with low dose rate brachytherapy (BT) for a PBN post RP. Methods: All 12 patients had biopsy confirmed cases of recurrent adenocarcinoma in the prostatic bed. At the time of PBN diagnosis, 2 patients had received EBRT, 2 patients had received ADT, and 1 patient had undergone HIFU. Patients were confirmed to have a negative CT and bone scan prior to salvage BT. All patients received salvage BT with I-125 prescribed to 144 Gray. Results: The median interval between RP and BT was 8 years (range 0.5- 17.9), median PSA prior to BT was 4.53 ng/ml (range 0.55-15.2), and the median age was 69 (range 59-86). Forty-two percent of patients had a PBN Gleason score of 8, 33% had a score of 7, and a score was not reported for 25% of patients due to prior EBRT or ADT use. The median follow up for this series is 26.5 months (range 1-69). At the time of this analysis, 10 patients were evaluable for biochemical failure (bF) (nadir+2) and distant metastases (DM). The one and two year rates of bF were 0% and 52%. There was no association between pre-BT PSA and bF, nor between pre-BT Gleason score and bF. Two patients subsequently developed DM at 17 months and 55 months after BT. The pelvic lymph nodes were the site of DM for both patients. The median PSA velocity post BT was -0.120 ng/ml/yr (range -1.404- 9.096). Five patients had a negative PSA velocity at last follow-up, while 4 had an increasing PSA velocity. Velocity could not be defined for 3 patients (insufficient PSA n=2, ADT n=1). To date, no gastrointestinal or urinary toxicities have been noted. Conclusions: Brachytherapy as a salvage treatment for a PBN appears to be well tolerated. The rates of bF and DM following salvage BT are comparable to those of salvage EBRT for this patient population. Intermediate-term biochemical control was attained in a sub-set of patients with declining PSA at last follow-up.