gebhart/patrepeval huggingface dataset:
A three-axis fast-tow digital Video Plankton Recorder for rapid surveys of plankton taxa and hydrography (2005)

A new Video Plankton Recorder (VPRII) has been developed for rapid surveys of plankton and seston in the size range of 100µm–1cm. The VPRII system includes: 1) a high-resolution digital camera (1Mpixel, 10-bits, 30Hz frame-rate), 2) a fast towfish capable of tow speeds up to 12 knots and 3-axis motion for automatic undulation and ship-wake avoidance, small diameter tow cable and winch for deployment on coastal vessels, and 3) new interface software (Visual Plankton) for automatic identification of plankton to major taxa and visualization of these taxa together with hydrographic data in real time. Camera and strobe optics are laboratory-adjusted to select the field-of-view (5–20mm), and depth-of-field is objectively calibrated using a tethered organism (e.g., copepod) and automatic focus-detection software. The VPRII towfish comprises a fuselage, a fixed main wing, and three servo-controlled tail fins: port and starboard for dive, climb, and roll control and rudder for lateral movement. Placement of the strobe (starboard wing-tip), camera (fuselage nose), and cantilevered tow-bridle minimize disturbance of the imaged volume. Compared with typical net surveys in shelf areas, the VPRII counts more plankton per station, quantifies ubiquitous fragile forms, automatically identifies plankton to major taxa and measures their size, quantifies scales of patchiness down to a few cm, and displays high-resolution distributions of plankton taxa and hydrography while underway. The VPRII is available to researchers via the Woods Hole Oceanographic Institution ship instrumentation pool.
Hardware-Efficient Node Processing Unit Architectures for Flexible LDPC Decoder Implementations (2018)

In low-density parity check (LDPC) decoder implementations, the architecture of the node processing units (NPUs) has a significant impact both on the hardware resource requirements and on the processing throughput. Additionally, some NPU architectures impose limitations on the decoder's support for intra- or interstandard LDPC code flexibility at run-time. In this brief, we present a generalised algorithmic method of constructing NPUs that support run-time flexibility while maintaining a low hardware resource requirement and high maximum operating frequency. FPGA-based synthesis results demonstrate that the proposed architecture offers a significantly improved hardware efficiency, when compared to two commonly employed alternatives.
Mycorrhiza helper bacteria (2016)

This chapter focuses on the Mycorrhiza Helper Bacteria (MHB), a generic name given to bacteria which stimulate the formation of mycorrhizal symbiosis. By extension, some bacterial strains that positively impact the functioning of mycorrhizal symbiosis are also called MHB. These bacteria have applicative interests, as they indirectly improve the health and growth of tree seedlings. MHB are not restricted to a specific type of ecosystem, but are rather generalist in the way that they associate with both herbaceous and woody mycorrhizal plants from boreal, temperate, arid and tropical ecosystems. However, understanding the molecular mechanisms and their specificities will help us to know more about the ecology of the MHB. The process of acquisition varies between fungal species; while ectomycorrhizal fungi most probably recurrently acquire them from the environment, the association between bacterial endosymbionts and Glomeromycota probably dates back to very ancient times, and has since been vertically transmitted.
Elastically Tunable Self‐Organized Organic Lasers (2011)

Organic lasers that rely on sinusoidal, tunable distributed-feedback gratings formed by self-organization of the surface of elastomeric PDMS are demonstrated. The lasing wavelength can be tuned by stretching. The simple fabrication of the lasers on potentially large areas enables entirely new applications such as a strain-sensing optical skin for structural health monitoring. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Novel X‐linked inhibitor of apoptosis inhibiting compound as sensitizer for TRAIL‐mediated apoptosis in chronic lymphocytic leukaemia with poor prognosis (2010)

Given that aggressive DNA damaging chemotherapy shows suboptimal efficacy in chronic lymphocytic leukaemia (CLL), alternative therapeutic approaches are needed. Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) is able to induce tumour-specific apoptosis. However, apoptosis might be inhibited by elevated levels of X-linked inhibitor of apoptosis (XIAP). Use of XIAP-inhibiting compounds might sensitize primary CLL cells towards TRAIL-mediated apoptosis. A novel small molecule, compound A (CA), an inhibitor of XIAP, was used in combination with TRAIL to induce apoptosis in primary CLL cells (n = 48). XIAP was significantly more highly expressed in primary CLL cells (n = 28) compared to healthy B cells (n = 16) (P = 0·02). Our data obtained by specific knock-down of XIAP by siRNA identified XIAP as the key factor conferring resistance to TRAIL in CLL. Combined treatment with CA/TRAIL significantly increased apoptosis compared to untreated (P = 8·5 × 10⁻¹⁰), solely CA (P = 4·1 × 10⁻¹²) or TRAIL treated (P = 4·8 × 10⁻¹⁰) CLL cells. CA rendered 40 of 48 (83·3%) primary CLL samples susceptible to TRAIL-mediated apoptosis. In particular, cells derived from patients with poor prognosis CLL (ZAP-70(+) , IGHV unmutated, 17p-) were highly responsive to this drug combination. Our highly-effective XIAP inhibitor CA, in concert with TRAIL, shows potential for the treatment of CLL cases with poor prognosis and therefore warrants further clinical investigation.
Synthesis and Properties of Supramolecular Ionic Networks (2008)

The synthesis of a supramolecular ionic network, its physical properties, and the use of this network property to form macroscopic porphyrin fibers are described. These ionic networks are compared to ionic liquids. Current ionic liquid compositions have a charge and molar ratio of 1:1 where an anionic species is matched with a cationic species; however, alteration of this molar ratio while maintaining the charge ratio of 1:1 by using multivalent cationic/anionic molecular pairs affords new ionically cross-linked networks with interesting properties.
An overview of rapamycin: from discovery to future perspectives (2016)

Rapamycin is an immunosuppressive metabolite produced from several actinomycete species. Besides its immunosuppressive activity, rapamycin and its analogs have additional therapeutic potentials, including antifungal, antitumor, neuroprotective/neuroregenerative, and lifespan extension activities. The core structure of rapamycin is derived from (4R,5R)-4,5-dihydrocyclohex-1-ene-carboxylic acid that is extended by polyketide synthase. The resulting linear polyketide chain is cyclized by incorporating pipecolate and further decorated by post-PKS modification enzymes. Herein, we review the discovery and biological activities of rapamycin as well as its mechanism of action, mechanistic target, biosynthesis, and regulation. In addition, we introduce the many efforts directed at enhancing the production of rapamycin and generating diverse analogs and also explore future perspectives in rapamycin research. This review will also emphasize the remarkable pilot studies on the biosynthesis and production improvement of rapamycin by Dr. Demain, one of the world's distinguished scientists in industrial microbiology and biotechnology.
A Versatile, Voltage-Pulse Based Read and Programming Circuit for Multi-Level RRAM Cells (2021)

In this work, we present an integrated read and programming circuit for Resistive Random Access Memory (RRAM) cells. Since there are a lot of different RRAM technologies in research and the process variations of this new memory technology often spread over a wide range of electrical properties, the proposed circuit focuses on versatility in order to be adaptable to different cell properties. The circuit is suitable for both read and programming operations based on voltage pulses of flexible length and height. The implemented read method is based on evaluating the voltage drop over a measurement resistor and can distinguish up to eight different states, which are coded in binary, thereby realizing a digitization of the analog memory value. The circuit was fabricated in the 130 nm CMOS process line of IHP. The simulations were done using a physics-based, multi-level RRAM model. The measurement results prove the functionality of the read circuit and the programming system and demonstrate that the read system can distinguish up to eight different states with an overall resistance ratio of 7.9.
Congruence and joint space width alterations of the medial compartment following lateral unicompartmental knee arthroplasty (2015)

Progressive degenerative changes in the medial compartment of the knee following lateral unicompartmental arthroplasty (UKA) remains a leading indication for revision surgery. The purpose of this study is to evaluate changes in the congruence and joint space width (JSW) of the medial compartment following lateral UKA. The congruence of the medial compartment of 53 knees (24 men, 23 women, mean age 13.1 years; sd 62.1) following lateral UKA was evaluated pre-operatively and six weeks post-operatively, and compared with 41 normal knees (26 men, 15 women, mean age 33.7 years; sd 6.4), using an Interactive closest point algorithm which calculated the congruence index (CI) by performing a rigid transformation that best aligns the digitised tibial and femoral surfaces. Inner, middle and outer JSWs were measured by sub-dividing the medial compartment into four quarters on pre- and post-operative, weight bearing tunnel view radiographs. The mean CI of knees following lateral UKA significantly improved from 0.92 (sd 0.06) pre-operatively to 0.96 (sd 0.02) (p < 0.001) six weeks post-operatively. The mean CI of the healthy control group was 0.99 sd 0.01. Post-operatively, the mean inner JSW increased (p = 0.006) and the outer decreased (p = 0.002). The JSW was restored post-operatively as no significant differences were noted in all three locations compared with the control group (inner JSW p = 0.43; middle JSW p = 0.019, outer JSW p = 0.51). Our data suggest that a well conducted lateral UKA may improve the congruence and normalise the JSW of the medial compartment, potentially preventing progression of degenerative change.
Feasibility of optimizing the dose distribution in lung tumors using fluorine‐18‐fluorodeoxyglucose positron emission tomography and single photon emission computed tomography guided dose prescriptions (2004)

The information provided by functional images may be used to guide radiotherapy planning by identifying regions that require higher radiation dose. In this work we investigate the dosimetric feasibility of delivering dose to lung tumors in proportion to the fluorine-18-fluorodeoxyglucose activity distribution from positron emission tomography (FDG-PET). The rationale for delivering dose in proportion to the tumor FDG-PET activity distribution is based on studies showing that FDG uptake is correlated to tumor cell proliferation rate, which is shown to imply that this dose delivery strategy is theoretically capable of providing the same duration of local control at all voxels in tumor. Target dose delivery was constrained by single photon emission computed tomography (SPECT) maps of normal lung perfusion, which restricted irradiation of highly perfused lung and imposed dose-function constraints. Dose-volume constraints were imposed on all other critical structures. All dose-volume/function constraints were considered to be soft, i.e., critical structure doses corresponding to volume/function constraint levels were minimized while satisfying the target prescription, thus permitting critical structure doses to minimally exceed dose constraint levels. An intensity modulation optimization methodology was developed to deliver this radiation, and applied to two lung cancer patients. Dosimetric feasibility was assessed by comparing spatially normalized dose-volume histograms from the nonuniform dose prescription (FDG-PET proportional) to those from a uniform dose prescription with equivalent tumor integral dose. In both patients, the optimization was capable of delivering the nonuniform target prescription with the same ease as the uniform target prescription, despite SPECT restrictions that effectively diverted dose from high to low perfused normal lung. In one patient, both prescriptions incurred similar critical structure dosages, below dose-volume/function limits. However, in the other patient, critical structure dosage from the nonuniform dose prescription exceeded dose-volume/function limits, and greatly exceeded that from the uniform dose prescription. Strict compliance to dose-volume/ function limits would entail reducing dose proportionality to the FDG-PET activity distribution, thereby theoretically reducing the duration of local control. Thus, even though it appears feasible to tailor lung tumor dose to the FDG-PET activity distribution, despite SPECT restrictions, strict adherence to dose-volume/function limits could compromise the effectiveness of functional image guided radiotherapy.
Prevention of spontaneous bleeding in dogs with haemophilia A and haemophilia B (2010)

Dogs with haemophilia A or haemophilia B exhibit spontaneous bleeding comparable with the spontaneous bleeding phenotype that occurs in humans with severe haemophilia. The phenotypic and genotypic characteristics of haemophilic dogs have been well-described, and such dogs are suitable for testing prophylactic protein replacement therapy and gene transfer strategies. In dogs with haemophilia, long-term effects on spontaneous bleeding frequency (measured over years) can be used as an efficacy endpoint in such studies. Although complete correction of coagulopathy has not been achieved, published data show that prophylactic factor replacement therapy and gene transfer can markedly reduce the frequency of spontaneous bleeding in haemophilic dogs. Further studies are currently ongoing.
Personalized ad recommendation systems for life-time value optimization with guarantees (2015)

In this paper, we propose a framework for using reinforcement learning (RL) algorithms to learn good policies for personalized ad recommendation (PAR) systems. The RL algorithms take into account the long-term effect of an action, and thus, could be more suitable than myopic techniques like supervised learning and contextual bandit, for modern PAR systems in which the number of returning visitors is rapidly growing. However, while myopic techniques have been well-studied in PAR systems, the RL approach is still in its infancy, mainly due to two fundamental challenges: how to compute a good RL strategy and how to evaluate a solution using historical data to ensure its safety before deployment. In this paper, we propose to use a family of off-policy evaluation techniques with statistical guarantees to tackle both these challenges. We apply these methods to a real PAR problem, both for evaluating the final performance and for optimizing the parameters of the RL algorithm. Our results show that a RL algorithm equipped with these off-policy evaluation techniques outperforms the myopic approaches. Our results also give fundamental insights on the difference between the click through rate (CTR) and life-time value (LTV) metrics for evaluating the performance of a PAR algorithm.
Persistence in Therapy With Risperidone and Aripiprazole in Pediatric Outpatients (2016)

The findings of this study show a similarity between the overall effectiveness of risperidone and aripiprazole in a real-life pediatric outpatient setting.
An automated COVID-19 triage pipeline using artificial intelligence based on chest radiographs and clinical data (2022)

While COVID-19 diagnosis and prognosis artificial intelligence models exist, very few can be implemented for practical use given their high risk of bias. We aimed to develop a diagnosis model that addresses notable shortcomings of prior studies, integrating it into a fully automated triage pipeline that examines chest radiographs for the presence, severity, and progression of COVID-19 pneumonia. Scans were collected using the DICOM Image Analysis and Archive, a system that communicates with a hospital's image repository. The authors collected over 6,500 non-public chest X-rays comprising diverse COVID-19 severities, along with radiology reports and RT-PCR data. The authors provisioned one internally held-out and two external test sets to assess model generalizability and compare performance to traditional radiologist interpretation. The pipeline was evaluated on a prospective cohort of 80 radiographs, reporting a 95% diagnostic accuracy. The study mitigates bias in AI model development and demonstrates the value of an end-to-end COVID-19 triage platform.
Hybrid imaging: a quantum leap in scientific imaging (2004)

ImagerLabs has advanced its patented next generation imaging technology called the Hybrid Imaging Technology (HIT) that offers scientific quality performance. The key to the HIT is the merging of the CCD and CMOS technologies through hybridization rather than process integration. HIT offers exceptional QE, fill factor, broad spectral response and very low noise properties of the CCD. In addition, it provides the very high-speed readout, low power, high linearity and high integration capability of CMOS sensors. In this work, we present the benefits, and update the latest advances in the performance of this exciting technology.
D6.5 Final Report on Communication and Dissemination Activities (2022)

The goal of the EU-funded UNICORE project is to develop a common code-base and toolchain that will enable software developers to rapidly create secure, portable, scalable, high-performance solutions starting from existing applications. The key to this is to compile an application into very light-weight virtual machines – known as unikernels – where there is no traditional operating system, only the specific bits of operating system functionality that the application needs. The resulting unikernels can then be deployed and run on standard high-volume servers or cloud computing infrastructure. This document reports on the achievements of the entire UNICORE project (Jan 2019-March 2022) for all the communication and dissemination executed by the Consortium. In addition, Year 3 and the 3 Months extension in 2022 are explained as well, as no deliverable has been submitted for this period.
Supplemental Figure 1 from PD-1 Restrains Radiotherapy-Induced Abscopal Effect (2023)

&lt;p&gt;Supplemental Figure 1. Synergistic effects of PD-1 and CTLA-4 blockade in enhancing antitumor abscopal effects.&lt;/p&gt;
Identification and recombinant expression of anandamide hydrolyzing enzyme from Dictyostelium discoideum (2012)

This study describes the first identification and characterisation of an anandamide hydrolyzing enzyme from Dictyostelium discoideum, suggesting the potential of Dictyostelium as a simple eukaryotic model system for studying mechanisms of action of any FAAH inhibitors as drug targets.
A tissue preparation to characterize uterine fibroid tissue properties for thermal therapies (2019)

This study developed an MR-compatible extracorporeal perfusion technique that effectively maintains tissue viability, allowing for the direct measurement of patient-specific MR, thermal, and acoustic property values for both fibroid and myometrium tissues. These measured tissue property values will enable further development and validation of treatment planning models that can be utilized during MRgFUS uterine fibroid treatments.
Phase I Study Assessing the Pharmacokinetic Profile, Safety, and Tolerability of a Single Dose of Ceftazidime-Avibactam in Hospitalized Pediatric Patients (2016)

This study aimed to investigate the pharmacokinetics (PK), safety, and tolerability of a single dose of ceftazidime-avibactam in pediatric patients. A phase I, multicenter, open-label PK study was conducted in pediatric patients hospitalized with an infection and receiving systemic antibiotic therapy. Patients were enrolled into four age cohorts (cohort 1, ≥12 to <18 years; cohort 2, ≥6 to <12 years; cohort 3, ≥2 to <6 years; cohort 4, ≥3 months to <2 years). Patients received a single 2-h intravenous infusion of ceftazidime-avibactam (cohort 1, 2,000 to 500 mg; cohort 2, 2,000 to 500 mg [≥40 kg] or 50 to 12.5 mg/kg [<40 kg]; cohorts 3 and 4, 50 to 12.5 mg/kg). Blood samples were collected to describe individual PK characteristics for ceftazidime and avibactam. Population PK modeling was used to describe characteristics of ceftazidime and avibactam PK across all age groups. Safety and tolerability were assessed. Thirty-two patients received study drug. Mean plasma concentration-time curves, geometric mean maximum concentration (Cmax), and area under the concentration-time curve from time zero to infinity (AUC0-∞) were similar across all cohorts for both drugs. Six patients (18.8%) reported an adverse event, all mild or moderate in intensity. No deaths or serious adverse events occurred. The single-dose PK of ceftazidime and avibactam were comparable between each of the 4 age cohorts investigated and were broadly similar to those previously observed in adults. No new safety concerns were identified. (This study has been registered at ClinicalTrials.gov under registration no. NCT01893346.).
Physical Adversarial Attacks Against End-to-End Autoencoder Communication Systems (2019)

We show that end-to-end learning of communication systems through deep neural network autoencoders can be extremely vulnerable to physical adversarial attacks. Specifically, we elaborate how an attacker can craft effective physical black-box adversarial attacks. Due to the openness (broadcast nature) of the wireless channel, an adversary transmitter can increase the block-error-rate of a communication system by orders of magnitude by transmitting a well-designed perturbation signal over the channel. We reveal that the adversarial attacks are more destructive than the jamming attacks. We also show that classical coding schemes are more robust than the autoencoders against both adversarial and jamming attacks.