Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic Microbiologic Methods in the GEMS-1 Case/Control Study

To understand the etiology of moderate-to-severe diarrhea among children in high mortality areas of sub-Saharan Africa and South Asia, we performed a comprehensive case/control study of children aged <5 years at 7 sites. Each site employed an identical case/control study design and each utilized a uniform comprehensive set of microbiological assays to identify the likely bacterial, viral and protozoal etiologies. The selected assays effected a balanced consideration of cost, robustness and performance, and all assays were performed at the study sites. Identification of bacterial pathogens employed streamlined conventional bacteriologic biochemical and serological algorithms. Diarrheagenic Escherichia coli were identified by application of a multiplex polymerase chain reaction assay for enterotoxigenic, enteroaggregative, and enteropathogenic E. coli. Rotavirus, adenovirus, Entamoeba histolytica, Giardia enterica, and Cryptosporidium species were detected by commercially available enzyme immunoassays on stool samples. Samples positive for adenovirus were further evaluated for adenovirus serotypes 40 and 41. We developed a novel multiplex assay to detect norovirus (types 1 and 2), astrovirus, and sapovirus. The portfolio of diagnostic assays used in the GEMS study can be broadly applied in developing countries seeking robust cost-effective methods for enteric pathogen detection.
Coherent storage of temporally multimode light using a spin-wave atomic frequency comb memory

We report on the coherent and multi-temporal mode storage of light using the full atomic frequency comb memory scheme. The scheme involves the transfer of optical atomic excitations in Pr3+:Y2SiO5 to spin waves in hyperfine levels using strong single-frequency transfer pulses. Using this scheme, a total of five temporal modes are stored and recalled on-demand from the memory. The coherence of the storage and retrieval is characterized using a time-bin interference measurement resulting in visibilities higher than 80%, independent of the storage time. This coherent and multimode spin-wave memory is promising as a quantum memory for light.
Kisspeptin Regulation of Genes Involved in Cell Invasion and Angiogenesis in First Trimester Human Trophoblast Cells

The precise regulation of extravillous trophoblast invasion of the uterine wall is a key process in successful pregnancies. Kisspeptin (KP) has been shown to inhibit cancer cell metastasis and placental trophoblast cell migration. In this study primary cultures of first trimester human trophoblast cells have been utilized in order to study the regulation of invasion and angiogenesis-related genes by KP. Trophoblast cells were isolated from first trimester placenta and their identity was confirmed by immunostaining for cytokeratin-7. Real-time quantitative RT-PCR demonstrated that primary trophoblast cells express higher levels of GPR54 (KP receptor) and KP mRNA than the trophoblast cell line HTR8Svneo. Furthermore, trophoblast cells also expressed higher GPR54 and KP protein levels. Treating primary trophoblast cells with KP induced ERK1/2 phosphorylation, while co-treating the cells with a KP antagonist almost completely blocked the activation of ERK1/2 and demonstrated that KP through its cognate GPR54 receptor can activate ERK1/2 in trophoblast cells. KP reduced the migratory capability of trophoblast cells in a scratch-migration assay. Real-time quantitative RT-PCR demonstrated that KP treatment reduced the expression of matrix metalloproteinase 1, 2, 3, 7, 9, 10, 14 and VEGF-A, and increased the expression of tissue inhibitors of metalloproteinases 1 and 3. These results suggest that KP can inhibit first trimester trophoblast cells invasion via inhibition of cell migration and down regulation of the metalloproteinase system and VEGF-A.
State of the Art on Monocular 3D Face Reconstruction, Tracking, and Applications

The computer graphics and vision communities have dedicated long standing efforts in building computerized tools for reconstructing, tracking, and analyzing human faces based on visual input. Over the past years rapid progress has been made, which led to novel and powerful algorithms that obtain impressive results even in the very challenging case of reconstruction from a single RGB or RGB‐D camera. The range of applications is vast and steadily growing as these technologies are further improving in speed, accuracy, and ease of use.
Touching a Stranger: Designing for Engaging Experience in Embodied Interaction

We present Mediated Body, an exploration into designing for engaging experience in embodied interaction. Mediated Body entails a Suit worn by a Performer engaging in social play with a Participant. The Performer and the Participant each wear a pair of headphones, and when they touch each other’s bare skin, they both hear a complex sound pattern. Our approach, which we call research-throughexplorative-design, is a combination of experimental design in the lab and explorative design in the field, where qualitative assessments are used to elicit transferable knowledge contributions. This paper represents a case study of this somewhat innovative research approach in action. On the topical level, our results include three artifact-level elements that contribute to engaging experience: connecting touch and audio with the right balance between direct and emergent responsivity, justifying bare-skin touch between strangers, and providing openended action props with non-trivial internal complexity. Moreover, we suggest three experiential qualities as analytical tools pertaining to engaging experience in embodied interaction: the duality of performative immersion, the “magic circle” of transformative social play, and the explorative nature of emergent meaning-making.
Slope Shape Effects on Erosion

Data on soil erosion at the slope scale is essentially limited to experiments on uniform slopes. The objective of this research was to measure the rates and patterns of erosion on complex shaped slope elements under controlled laboratory conditions where surface morphology changes could be carefully quantified. Artificial rainfall was applied for 90 min to a silt loam soil in a 4 by 4 m box. Five slope shapes were formed: uniform, concave-linear, convex-linear, nose slope, and head slope. Digital elevations models (DEMs) of the surface were measured using photogrammetry after 0, 10, 20, 40, 60, and 90 min. Slope shape had a significant impact on rill patterns, sediment yield, and runoff production. The uniform, nose, and convex-linear slopes yielded more sediment than the concave-linear and head slopes, where sediment deposited on toeslopes. Soil topography led to flow convergence and divergence, resulting in a nonuniform distribution of rill spacing and efficiency. The degree of rill incision was related to slope steepness and length, and rill success was related to the contribution area of the rill. Drainage density approached a similar value for all networks during the experiments. Development of the drainage system was similar to the development of optimum channel networks, in that during the evolution of the rill network energy expenditure was reduced. This indicated that energy expenditure was a quantifiable measure of network development and self-organization.
User Evaluation of a Smartphone Application for Anticoagulation Therapy

Anticoagulation therapy with Warfarin is used for specific cardiovascular diseases to control the ability of blood clotting. Traditional ways of self-management therapy are based on paper forms and procedures. This paper presents an evaluation of the smartphone application Warfarin Guide, a computer-assisted decision-support system used to help patients in their management of anticoagulation therapy related to International Normalized Ratio (INR) values. The evaluation consisted of a usability test with 4 participants and a field test with 14 participants who used the application at home during four months. A mixed methods research approach included quantitative and qualitative analysis of the test results. The results showed that participants evaluated the Warfarin Guide as 'useful' for self-management of anticoagulation therapy, reporting key issues for further improvement.
Duration of methicillin-resistant Staphylococcus aureus colonization after diagnosis: A four-year experience from southern Sweden

Abstract Background: The duration of colonization with methicillin-resistant Staphylococcus aureus (MRSA) is not well known and there is debate as to whether a patient colonized with MRSA ever can be defined as ‘MRSA-negative’. Methods: Since 2003 all notified MRSA cases have been systematically followed in Skåne County, southern Sweden. Cultures are taken from the nares, throat, perineum and possible skin lesions. Contact tracing is conducted. The screening program continues as long as cultures are positive and then until 1 y of consecutive negative cultures for MRSA is completed. Results: Of the 578 MRSA cases during 2003–2006, 535 were included in this retrospective study. The median duration of colonization with MRSA was 5.9 months. Having household contacts with MRSA, young age, spa-type t002 and colonization in 2 or more locations, were significantly associated with a longer duration of colonization. Having a clinical infection treated with antibiotics (compared to clinical infection with no antibiotic treatment or asymptomatic carriage) was significantly associated with a shorter carriage time. Eradication treatment was associated with a shorter carriage time. Conclusion: These results may have implications for the management of patients with MRSA carriage. The study indicates that MRSA carriage can be defined as ‘negative’ in a follow-up program and shows the importance of performing contact tracing among household members.
Maize Stem Response to Long-Term Attack by Sesamia nonagrioides

Plants defend themselves against herbivores by activating a plethora of genetic and biochemical mechanisms aimed at reducing plant damage and insect survival. The short-term plant response to insect attack is well understood, but less is known about the maintenance of this response over time. We performed transcriptomic and metabolomics analyses in order to identify genes and metabolites involved in the long-term response of maize to attack by the corn borer Sesamina nonagrioides. To determine the role of elicitors present in caterpillar secretions, we also evaluated the response of maize stem challenged with insect regurgitates. The integrative analysis of the omics results revealed that the long-term response in maize is characterized by repression of the primary metabolism and a strong redox response, mainly mediated by germin-like proteins to produce anti-nutritive and toxic compounds that reduce insect viability, and with the glutathione–ascorbate cycle being crucial to minimize the adverse effects of reactive oxygen species (ROS) on the plant. Our results suggest that different defense mechanisms are involved in the long-term response compared to those reported during the early response. We also observed a marginal effect of the caterpillar regurgitates on the long-term defensive response.
Design of virtual synchronous generators with enhanced frequency regulation and reduced voltage distortions

In modern power systems where the penetration of renewable energy resources is normally high, functions of voltage and frequency support are supposed to be taken over by virtual synchronous generators (VSGs) or virtual synchronous machines (VSMs), i.e., grid-connected inverters which are controlled to mimic the terminal characteristics of synchronous generators. In this paper, the comprehensive design of VSGs is provided in detail. The proposed control scheme consists of two control loops. The inner-loop voltage and current controller is designed in the discrete j-domain to guarantee system stability and voltage control with low distortions, while the design of the outer-loop frequency and power controller is performed in the continuous s-domain to be in consistence with the conventional power system frequency regulation models. With the proposed design method, various control objectives, e.g., resonance damping, voltage support, primary frequency regulation, secondary frequency regulation, and virtual inertia, can easily be achieved and evaluated. Finally, experimental results obtained from a 500-W three-phase virtual synchronous generator prototype are presented to verify the effectiveness of the proposed design method.
Sarcopenia and cachexia in the era of obesity: clinical and nutritional impact

Our understanding of body composition (BC) variability in contemporary populations has significantly increased with the use of imaging techniques. Abnormal BC such as sarcopenia (low muscle mass) and obesity (excess adipose tissue) are predictors of poorer prognosis in a variety of conditions or clinical situations. As a catabolic illness, a defining feature of cancer is muscle loss. Although the conceptual model of wasting in cancer is typically conceived as involuntary weight loss leading to low body weight, recent studies have shown that both sarcopenia and cachexia can be present with obesity. The combination of low muscle and high adipose tissue (sarcopenic obesity) is an emerging abnormal BC phenotype prevalent across the body weight, and hence BMI spectra. Sarcopenia and sarcopenic obesity in cancer are in most instances occult conditions, which have been independently associated with higher incidence of chemotherapy toxicity, shorter time to tumour progression, poorer outcomes of surgery, physical impairment and shorter survival. Although the mechanisms are yet to be fully understood, the associations with poorer clinical outcomes emphasise the value of nutritional assessment as well as the need to develop appropriate interventions to countermeasure abnormal BC. Sarcopenia and sarcopenic obesity create diverse nutritional requirements, highlighting the compelling need for a more comprehensive and differentiated understanding of energy and protein requirements in this heterogeneous population.
Recurrent Neural Networks With Auxiliary Memory Units

Memory is one of the most important mechanisms in recurrent neural networks (RNNs) learning. It plays a crucial role in practical applications, such as sequence learning. With a good memory mechanism, long term history can be fused with current information, and can thus improve RNNs learning. Developing a suitable memory mechanism is always desirable in the field of RNNs. This paper proposes a novel memory mechanism for RNNs. The main contributions of this paper are: 1) an auxiliary memory unit (AMU) is proposed, which results in a new special RNN model (AMU-RNN), separating the memory and output explicitly and 2) an efficient learning algorithm is developed by employing the technique of error flow truncation. The proposed AMU-RNN model, together with the developed learning algorithm, can learn and maintain stable memory over a long time range. This method overcomes both the learning conflict problem and gradient vanishing problem. Unlike the traditional method, which mixes the memory and output with a single neuron in a recurrent unit, the AMU provides an auxiliary memory neuron to maintain memory in particular. By separating the memory and output in a recurrent unit, the problem of learning conflicts can be eliminated easily. Moreover, by using the technique of error flow truncation, each auxiliary memory neuron ensures constant error flow during the learning process. The experiments demonstrate good performance of the proposed AMU-RNNs and the developed learning algorithm. The method exhibits quite efficient learning performance with stable convergence in the AMU-RNN learning and outperforms the state-of-the-art RNN models in sequence generation and sequence classification tasks.
Plasma YKL-40 Elevation on Admission and Follow-Up Is Associated with Diastolic Dysfunction and Mortality in Patients with Acute Myocardial Infarction

Objective The aim of the study was to determine an association between the plasma YKL-40 level and echocardiographic left ventricle systolic and diastolic function parameters in patients with acute myocardial infarction. Subjects and Methods The study included 46 patients with acute myocardial infarction. Serum brain natriuretic protein (BNP) and YKL-40 levels were analyzed on admission and after one month. Left ventricle systolic and diastolic functions and Tei index were computed by transthoracic echocardiography. Results Plasma YKL-40 was significantly higher in patients with acute myocardial infarction (AMI) (101.7 μg/L versus 34 μg/L, resp., p < 0.001) and remained higher than in healthy subjects after one month. The levels of YKL-40 on admission were correlated with log BNP on admission (r=0.41, p=0.004), Tei index (r=0.44, p=0.002), left atrium volume index (r=0.32, p=0.02), and mitral septal annular E/e′ (r=0.44, p=0.003). Death was more frequently observed in patients with plasma YKL-40 above the median value than in those with plasma YKL-40 below the median value (p=0.001; OR = 13.6 (2.5–72.3)). Conclusion YKL-40 elevations in patients with AMI remain at least one month and are associated with serum BNP elevations, diastolic dysfunction, and long-term increased overall mortality. It has prognostic importance in patients with AMI.
Testing for NRAS Mutations in Serous Borderline Ovarian Tumors and Low-Grade Serous Ovarian Carcinomas

The Idylla NRAS Mutation Test, performed on the Biocartis Idylla system, is an in vitro diagnostic tool for the qualitative assessment of 18 NRAS mutations in codons 12, 13, 59, 61, 117, and 146. Low-grade serous ovarian cancer (LGSC) represents less than 10% of all serous ovarian carcinomas. LGSCs are believed to arise from preexisting cystadenomas or serous borderline tumors (SBOTs) that eventually progress to an invasive carcinoma. The molecular analysis of cancer-causing mutations and the development of targeted biological therapies constitute a milestone in the diagnosis and therapy of ovarian malignancies. According to some authors, NRAS may be an important oncogene for the progression of SBOT to a frankly invasive disease. The primary aim of this study was to verify if a fully integrated, real-time PCR-based Idylla system can be used for the rapid determination of the NRAS mutation status in patients with serous borderline ovarian tumors and low-grade serous ovarian carcinomas. The study included tissue specimens from 12 patients with histopathologically verified ovarian masses, operated on at the Department of Obstetrics and Gynecology, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz (Poland), between January 2009 and June 2012. The mean age of the study patients was 52.5 years (range 27–80 years). NRAS mutation in codon 13 (G13D, p.Gly13Asp; nucleotide: c.38G>A) was found in one patient, a woman with low-grade serous ovarian carcinoma. To the best of our knowledge, our experiment was the first published study using the novel Idylla NRAS Mutation Test for the evaluation of ovarian tumors in a clinical setting. The Idylla platform is an interesting ancillary first-line rapid and fully automated instrument to detect NRAS mutations in SBOTs and LGSCs. However, the clinical usefulness of this method still needs to be verified in larger groups of cancer patients.
CCNE1 amplification is associated with aggressive potential in endometrioid endometrial carcinomas

The clinicopathological significance of amplification was investigated of the gene encoding cyclin E (CCNE1) and we assessed whether CCNE1 was a potential target in endometrioid endometrial carcinomas. CCNE1 amplification and CCNE1 or F-box and WD repeat domain-containing 7 (FBXW7) expression in endometrial endometrioid carcinoma was assessed by immunohistochemistry and fluorescence in situ hybridization. CCNE1 knockdown by small interfering RNA (siRNA) was used to assess the CCNE1 function. The results showed that CCNE1 amplification was present in 9 (8.3%) of 108 endometrial carcinomas. CCNE1 amplification was correlated with high histological grade (Grade 3; P=0.0087) and lymphovascular space invasion (P=0.0258). No significant association was observed between CCNE1 amplification and FIGO stage (P=0.851), lymph node metastasis (P=0.078), body mass index (P=0.265), deep myometrial invasion (P=0.256), menopausal status (P=0.289) or patient age (P=0.0817). CCNE1 amplification was significantly correlated with shorter progression-free and overall survival (P=0.0081 and 0.0073, respectively). CCNE1 protein expression or loss of FBXW7 expression in endometrial endometrioid carcinoma tended to be correlated with shorter progression-free and overall survival; however, this difference was not statistically significant. Multivariate analysis showed that CCNE1 amplification was an independent prognostic factor for overall survival but not for progression-free survival (P=0.0454 and 0.2175, respectively). Profound growth inhibition was observed in siRNA-transfected cancer cells with endogenous CCNE1 overexpression compared with that in cancer cells having low CCNE1 expression. CCNE1 amplification was independent of p53, HER2, MLH1 and ARID1A expression but dependent on PTEN expression in endometrial carcinomas. These findings indicated that CCNE1 amplification was critical for the survival of endometrial endometrioid carcinomas. Furthermore, the effects of CCNE1 knockdown were dependent on the CCNE1 expression status, suggesting that CCNE1-targeted therapy may be beneficial for patients with endometrial endometrioid carcinoma having CCNE1 amplification.
Underuse of clozapine in treatment-resistant schizophrenia †

Up to a third of patients with schizophrenia develop treatment resistance. Clozapine has been established as the most effective antipsychotic medication for treatment-resistant schizophrenia. However, it is significantly underutilised in this population. Possible reasons include clinicians' lack of experience with the drug and negative attitudes towards it. African-Caribbean patients are less likely to be treated with clozapine compared with their White counterparts and more likely to have treatment discontinued due to perceived risk of agranulocytosis. This paper discusses the current evidence relating to the underuse of clozapine and factors responsible for this.
Wireless Secure Communication With Beamforming and Jamming in Time-Varying Wiretap Channels

For physical layer security with multiple antennas over wireless channels, we consider an artificial noise-aided secure beamforming system. A transmitter can send the confidential information to the legitimate user more securely without eavesdropping when an artificial jamming signal interfering eavesdroppers is transmitted with the confidential information signal. The transmitter splits its transmit power for both the information and jamming signals with a power splitting factor. Under such a system model, we investigate the impacts on secrecy performance of a power splitting factor, the numbers of antennas and eavesdroppers, and noise variance at the legitimate receivers and eavesdroppers by analyzing the expected secrecy rate. The optimal power splitting factor and limiting secrecy rate with large number of antennas are also derived. Moreover, we examine the expected secrecy rate loss caused by channel variation over time. It is shown that the secrecy rate loss is independent of system parameters like a power splitting factor, the numbers of antennas and eavesdroppers in a high signal to interference plus noise ratio (SINR) region. In a low SINR region, on the other hand, the secrecy rate loss changes with system parameters. Simulation results verify these observations on ergodic secrecy rate and its loss due to time-varying channels.