Miracle-dz/UniFAR-FTUs huggingface dataset:
The validity of current guidelines regarding surgical management of patients with gastric neuroendocrine neoplasms type 1: a report of a series of seven patients

OBJECTIVE: Gastric neuroendocrine neoplasms Type 1 (GEN type 1) are mostly localized indolent tumors, with only a minority developing lymph node or distant metastasis. Although they are usually managed conservatively, large, invasive, recurrent and grade 2 lesions may require surgical treatment. The aim of this case series is to evaluate the validity of current guidelines regarding surgical management of patients with GEN type 1. CASES: Seven patients (5 female) with GEN type 1 underwent peri-gastric lymphadenectomy when at least one of the following criteria employed in previous guidelines was present: (i) multiple recurrent lesions, (ii) lesions with positive margins following endoscopic resection, (iii) lesions with malignant potential (deep gastric parietal wall invasion, lymph node enlargement, Ki67 proliferative index >2%), or (iv) presence of metastatic disease. Four patients met one and three two of the previously defined criteria; fifteen to thirty-six peri-gastric lymph nodes were resected. Following surgery there was no alteration in tumor staging status compared to pre-surgical staging. During a median follow-up of 34 months, all patients remain without any evidence of disease recurrence. CONCLUSION: Peri-gastric lymphadenectomy did not prove to be necessary for localized GEN type 1, neither for staging nor for therapeutical reasons. Further parameters need to be evaluated to identify the small subset of patients that will develop more aggressive disease.
Morpho-z: improving photometric redshifts with galaxy morphology

We conduct a comprehensive study of the effects of incorporating galaxy morphology information in photometric redshift estimation. Using machine learning methods, we assess the changes in the scatter and outlier fraction of photometric redshifts when galaxy size, ellipticity, Sersic index, and surface brightness are included in training on galaxy samples from the SDSS and the CFHT Stripe-82 Survey (CS82). We show that by adding galaxy morphological parameters to full ugriz photometry, only mild improvements are obtained, while the gains are substantial in cases where fewer passbands are available. For instance, the combination of grz photometry and morphological parameters almost fully recovers the metrics of 5-band photometric redshifts. We demonstrate that with morphology it is possible to determine useful redshift distribution N(z) of galaxy samples without any colour information. We also find that the inclusion of quasar redshifts and associated object sizes in training improves the quality of photometric redshift catalogues, compensating for the lack of a good star-galaxy separator. We further show that morphological information can mitigate biases and scatter due to bad photometry. As an application, we derive both point estimates and posterior distributions of redshifts for the official CS82 catalogue, training on morphology and SDSS Stripe-82 ugriz bands when available. Our redshifts yield a 68th percentile error of 0.058(1 + z), and a outlier fraction of 5.2 per cent. We further include a deep extension trained on morphology and single i-band CS82 photometry.
Genetic Identification of Communist Crimes’ Victims (1944–1956) Based on the Analysis of One of Many Mass Graves Discovered on the Powazki Military Cemetery in Warsaw, Poland

As the result of the communist terror in Poland, during years 1944–1956 more than 50,000 people died. Their bodies were buried secretly, and most places are still unknown. The research presents the results of identification of people buried in one of many mass graves, which were found at the cemetery Powązki Military in Warsaw, Poland. Exhumation revealed the remains of eight people, among which seven were identified genetically. Well‐preserved molars were used for the study. Reference material was collected from the closest living relatives. In one case, an exhumation of victim's parents had to be performed. DNA from swabs was extracted with a PrepFiler® BTA Forensic DNA Extraction Kit and organic method. Autosomal, Y‐STR amplification, and mtDNA sequencing were performed. The biostatistical calculations resulted in LR values from 1608 to 928 × 1018. So far, remains of more than 50 victims were identified.
Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

ABSTRACT In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota. IMPORTANCE The composition of the raw milk microbiota is an important consideration from both a spoilage perspective and a food safety perspective and has implications for milk targeted for direct consumption and for downstream processing. Factors that influence contamination have been examined previously, primarily through the use of culture-based techniques. We describe here the extensive application of high-throughput DNA sequencing technologies to study the relationship between the milk production environment and the raw milk microbiota. The results show that the environment in which the herd was kept was the primary driver of the composition of the milk microbiota composition.
Infection in the Newborn

after ^m^tted from the hospital district and elsewhere shortly the' ! nhThus, 8075 infants passed through the hospital in ^ under review : 382 of these infants died in the hospital ifiajof ? a m? nt^ birth ; but it must be borne in mind that the vast the ri^ ? f infants are discharged from a maternity hospital in bpf? SeC? n<^ half of the second week of life, and some of these die More t-c* 1 ? asSe eaching the age of one month. The cause of death was ^ *n 369 of the fatal cases by reviewing all the obstetrical,
Selection maintains signaling function of a highly diverged intrinsically disordered region

Significance Intrinsically disordered regions (IDRs) are widespread, have diverse functions, and are involved in human disease. Because standard sequence analysis methods identify little sequence homology in IDRs, it is not currently understood whether (or how) the functions of these protein regions are preserved over evolution. Here we show that orthologous IDRs can preserve regulatory functions despite near-complete sequence divergence. This suggests that natural selection maintains aggregate molecular properties in IDRs, which we propose to be quantitative traits. Consistent with this, we find signatures of stabilizing selection on the electrostatic properties of IDRs. Thus, in analogy to the rapid evolution of noncoding DNA in eukaryotic enhancers, divergence in primary amino acid sequence does not imply functional divergence in IDRs. Intrinsically disordered regions (IDRs) are characterized by their lack of stable secondary or tertiary structure and comprise a large part of the eukaryotic proteome. Although these regions play a variety of signaling and regulatory roles, they appear to be rapidly evolving at the primary sequence level. To understand the functional implications of this rapid evolution, we focused on a highly diverged IDR in Saccharomyces cerevisiae that is involved in regulating multiple conserved MAPK pathways. We hypothesized that under stabilizing selection, the functional output of orthologous IDRs could be maintained, such that diverse genotypes could lead to similar function and fitness. Consistent with the stabilizing selection hypothesis, we find that diverged, orthologous IDRs can mostly recapitulate wild-type function and fitness in S. cerevisiae. We also find that the electrostatic charge of the IDR is correlated with signaling output and, using phylogenetic comparative methods, find evidence for selection maintaining this quantitative molecular trait despite underlying genotypic divergence.
PROHIBITIN3 Forms Complexes with ISOCHORISMATE SYNTHASE1 to Regulate Stress-Induced Salicylic Acid Biosynthesis in Arabidopsis1[OPEN]

A PROHIBITIN family protein promotes salicylic acid production via the isochorismate pathway in response to stress. Salicylic acid (SA) is a major defense signal in plants. In Arabidopsis (Arabidopsis thaliana), the chloroplast-localized isochorismate pathway is the main source of SA biosynthesis during abiotic stress or pathogen infections. In the first step of the pathway, the enzyme ISOCHORISMATE SYNTHASE1 (ICS1) converts chorismate to isochorismate. An unknown enzyme subsequently converts isochorismate to SA. Here, we show that ICS1 protein levels increase during UV-C stress. To identify proteins that may play roles in SA production by regulating ICS1, we analyzed proteins that coimmunoprecipitated with ICS1 via mass spectrometry. The ICS1 complexes contained a large number of peptides from the PROHIBITIN (PHB) protein family, with PHB3 the most abundant. PHB proteins have diverse biological functions that include acting as scaffolds for protein complex formation and stabilization. PHB3 was reported previously to localize to mitochondria. Using fractionation, protease protection, and live imaging, we show that PHB3 also localizes to chloroplasts, where ICS1 resides. Notably, loss of PHB3 function led to decreased ICS1 protein levels in response to UV-C stress. However, ICS1 transcript levels remain unchanged, indicating that ICS1 is regulated posttranscriptionally. The phb3 mutant displayed reduced levels of SA, the SA-regulated protein PR1, and hypersensitive cell death in response to UV-C and avirulent strains of Pseudomonas syringae and, correspondingly, supported increased growth of P. syringae. The expression of a PHB3 transgene in the phb3 mutant complemented all of these phenotypes. We suggest a model in which the formation of PHB3-ICS1 complexes stabilizes ICS1 to promote SA production in response to stress.
The development of the University of Jordan word recognition test

Abstract Objective: To develop and validate a digitally recorded speech test battery to assess speech perception in Jordanian Arabic-speaking adults. Design: Selected stimuli were digitally recorded and were divided into four lists of 25 words each. Speech audiometry was completed for all listeners. Participants were divided into two equal groups of 30 listeners each with equal male to female ratio. The first group of participants completed speech reception thresholds (SRTs) and word recognition testing on each of the four lists using a fixed intensity. The second group of listeners was tested on each of the four lists at different intensity levels in order to obtain the performance-intensity function. Study sample: Sixty normal-hearing listeners in the age range of 19–25 years. All participants were native speakers of Jordanian Arabic. Results: Results revealed that there were no significant differences between SRTs and pure tone average. Additionally, there were no differences across lists at multiple intensity levels. Conclusions: In general, the current study was successful in producing recorded speech materials for Jordanian Arabic population. This suggests that the speech stimuli generated by this study are suitable for measuring speech recognition in Jordanian Arabic-speaking listeners.
Simultaneous finding of chronic lymphocytic leukemia and residual hairy cell leukemia using a lymphocyte‐binding anti‐CD antibody microarray

The morphologic diagnosis of hairy cell leukemia coexisting with another lymphoproliferative disorder is hindered by the small size of hairy cell population. It can be simplified by presorting peripheral blood mononuclear cell using an anti‐CD antibody microarray on transparent support (including anti‐CD11c, CD25, CD103, and CD123) before their morphology analysis.
Lead-Free Relaxor Ferroelectrics

Feature size is a natural determinant of material properties. Its design offers the technological perspectives for material improvement. Grain size, crystallite size, domain width, and structural defects of different nature constitute the classical design elements. Common ferroelectric ceramics contain micrometer grain sizes and submicrometer domain widths. Domain wall mobility is a major contribution to their macroscopic material properties providing approximately half of the macroscopic output in optimized materials. The extension into the dynamic nanoworld is provided by relaxor ferroelectrics. Ionic and nanoscale field disorders form the base to a state with natural nanometer-size polar structures even in bulk materials. These polar structures are highly mobile and can dynamically change over several orders of magnitude in time and space being extremely sensitive to external stimuli. This yields among the largest dielectric and piezoelectric constants known. In this feature article, we want to outline how lead-free relaxors will offer a route to an environmentally safer option in this outstanding material class. Properties of uniaxial, planar, and volumetric relaxor compositions will be discussed. They provide a broader and more interesting scope of physical properties and features than the classical lead-containing relaxor compositions.
Genome Mining of the Lipopeptide Biosynthesis of Paenibacillus polymyxa E681 in Combination with Mass Spectrometry: Discovery of the Lipoheptapeptide Paenilipoheptin

Paenibacillus polymyxa strains are qualified for agro‐biotechnological uses such as plant growth promotion and for biocontrol strategies against deleterious phytopathogenic competitors in the soil depending on their attractive arsenal of bioactive compounds. Moreover, they are potent producers of antibiotics for medical applications. To identify new products of such organisms, genome mining strategies in combination with mass spectrometry are the methods of choice. Herein, we performed such studies with the Paenibacillus strain E681. Bioinformatic evaluation of its genome sequence revealed four gene clusters A–D encoding nonribosomal peptide synthetases (NRPSs). Accordingly, four lipopeptide families were detected by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). Clusters A and D codify the well known fusaricidins and polymyxins. A yet‐unknown lipoheptapeptide was discovered and structurally characterized by de novo sequencing by using MALDI‐LIFT‐TOF/TOF MS. It was designated as paenilipoheptin. From structure predictions we infer that the production of this agent is encoded by gene cluster C. Gene cluster B encodes the synthesis of tridecaptins, a family of open‐chain lipotridecapeptides. Strain E681 produces new subspecies of such compounds (tridecaptins E) showing variations both in their fatty‐acid part as well as in their peptide part.
Modeling Missed Care: Implications for Evidence‐Based Practice

BACKGROUND There is a growing nursing literature that views missed care as an inevitable consequence of work intensification associated with the rationing of nursing and material resources available to deliver care. Global studies recognize that missed care is now ubiquitous, although studies tend to be conducted in one region, rather than nationwide. This study seeks to understand the Australian context of missed care. AIMS To explore self-reported reasons for missed care and to identify the main factors for predicting missed care within a sample of Australian nurses and midwives working in public and private hospitals in New South Wales, Victoria, Tasmania, and South Australia. METHODS A nonexperimental, descriptive method using Kalisch's (2006) MISSCARE survey was used. Responses from 1,195 nursing and midwifery staff with differing qualifications, English language skills, and Australian employment settings were analyzed using Rasch analysis and then modeled using the Structural Equation Modeling. RESULTS The frequency of missed care on the morning shift directly impacted on higher priority care missed during the afternoon shift. Staff skill mix imbalances and perceived inadequacy of staff numbers for the work demands further exacerbated all aspects of care during afternoon shifts. Other major factors associated with missed care were the different clinical work settings and staff to patient ratios. LINKING EVIDENCE TO ACTION The incidences, types, and reasons behind missed care are a multidimensional construct which can be predicted when known significant factors behind missed care are simultaneously accounted for.
On the Reconstruction of Face Images from Deep Face Templates

State-of-the-art face recognition systems are based on deep (convolutional) neural networks. Therefore, it is imperative to determine to what extent face templates derived from deep networks can be inverted to obtain the original face image. In this paper, we study the vulnerabilities of a state-of-the-art face recognition system based on template reconstruction attack. We propose a neighborly de-convolutional neural network (NbNet) to reconstruct face images from their deep templates. In our experiments, we assumed that no knowledge about the target subject and the deep network are available. To train the NbNet reconstruction models, we augmented two benchmark face datasets (VGG-Face and Multi-PIE) with a large collection of images synthesized using a face generator. The proposed reconstruction was evaluated using type-I (comparing the reconstructed images against the original face images used to generate the deep template) and type-II (comparing the reconstructed images against a different face image of the same subject) attacks. Given the images reconstructed from NbNets, we show that for verification, we achieve TAR of 95.20 percent (58.05 percent) on LFW under type-I (type-II) attacks @ FAR of 0.1 percent. Besides, 96.58 percent (92.84 percent) of the images reconstructed from templates of partition fa (fb) can be identified from partition fa in color FERET. Our study demonstrates the need to secure deep templates in face recognition systems.
Use of Social Media for Academic Purposes in China

In this article, we summarize social media in the academic context and contrast the differences between social media usage patterns in China and the United States. We describe our research methods and present the final results of our investigation. Our specific contribution is to clearly delineate the unique social media ecosystem as found in mainland China and how it is used in academic settings. Social media is helpful for supporting auxiliary academic activities such as knowledge dissemination and maintaining existing work and social relationships but is not a suitable way for people to obtain information that are necessary to foster research collaboration due to trust and privacy concerns. The expectation that social media might support academic relationship building has generally failed. Participants also reported being overwhelmed by the lack of work and life balance due to the fact that social media platforms have been adopted by their academic institutions as the official communication channel for work. We suggest ways to leverage social media to promote academic activities while avoiding the pitfalls identified in this paper.
CFD Simulation of Computer Room Air Conditioning : Our 2 D Navier-Stokes Solver coupled with Energy Equation vs . Fluent Simulation

This paper presents 2D computational fluid dynamic (CFD) simulation models of the computer room air conditioning system (CRAC) used for a data center. The models were developed with our own Navier-Stokes solver as well as Fluent to investigate the airflow patterns as well as temperature distribution inside the data center. Two cases with two different inlet velocities were compared to see a better CRAC configurations. The lid-driven cavity model was also developed with our own solver and Fluent to verify the appropriate implementation of energy equations in our own solver. The results show that supply air velocity with 45 degrees to the inlet has better cooling performance than that perpendicular to the inlet. In addition, comparisons on airflow patterns between our own solver and Fluent demonstrate that the trend of air velocity is similar even if values are different. Moreover, temperature distribution of the data center under steady state with our own solver have similar pattern to the result from Fluent.
Assessing rugby place kick performance from initial ball flight kinematics: development, validation and application of a new measure

Abstract The appropriate determination of performance outcome is critical when appraising a performer’s technique. Previous studies of rugby place kicking technique have typically assessed performance based on ball velocity, but this is not the sole requirement. Therefore, a mathematical model of rugby place kick ball flight was developed to yield a single measure more representative of true performance. The model, which requires only initial ball flight kinematics, was calibrated and validated using empirical place kick data, and found to predict ball position with a mean error of 4.0% after 22 m of ball flight. The model was then applied to the performances of 33 place kickers. The predicted maximum distance, a single performance measure which accounted for initial ball velocity magnitude and direction, and spin, was determined using the model and was compared against ball velocity magnitude. A moderate association in the rank-order of the kicks between these two measures (ρ = 0.52) revealed that the relative success of the kicks would be assessed differently with each measure. The developed model provides a representative measure of place kick performance that is understandable for coaches, and can be used to predict changes in performance outcome under different ball launch or environmental conditions.