Miracle-dz/UniFAR-FTUs huggingface dataset:
A Culture-Independent Analysis of the Microbiota of Female Interstitial Cystitis/Bladder Pain Syndrome Participants in the MAPP Research Network

We surveyed urine microbiota of females diagnosed with interstitial cystitis/bladder pain syndrome (IC/BPS) and matched control participants enrolled in the National Institutes of Health (NIH) Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) Research Network using the culture-independent methodology. Midstream urine specimens were analyzed with the Plex-ID molecular diagnostic platform that utilizes polymerase chain reaction–electrospray ionization–time-of-flight–mass spectrometry (PCR-ESI-TOF MS) to provide a comprehensive identification of bacterial and select fungal species. IC/BPS and control participants were evaluated for differences (presence, diversity, and abundance) in species and genus. Urine specimens obtained from 181 female IC/BPS and 182 female control participants detected a total of 92 species (41 genera). Mean (SD) species count was 2.49 (1.48) and 2.30 (1.28) among IC/BPS and control participants, respectively. Overall species composition did not significantly differ between IC/BPS and control participants at any level (p = 0.726 species level, p = 0.222 genus level). IC/BPS participants urine trended to an overabundance of Lactobacillus gasseri (p = 0.09) detected but had a lower prevalence of Corynebacterium compared with control participants (p = 0.002). The relative abundance data analysis mirrored the prevalence data differences with no significant differences in most species or genus abundance other than Lactobacillus gasseri and Corynebacterium (p = 0.08 and p = 0.001, respectively). No cause and/or effect conclusion can be drawn from this observation, but it suggests that a more comprehensive evaluation (vaginal, bowel, catheterized bladder and/or tissue-based specimens) of the lower urinary tract microbiota in IC/BPS patients is warranted.
Determination of Vehicle Speed from Recorded Video Using Reverse Projection Photogrammetry and File Metadata

The prevalence of security and in‐car video has increased the number of motor vehicle accidents captured on digital video. However, inconsistencies in how to accurately determine time and distance for vehicle speed has led to examinations with varying results. A potential solution for calculating time intervals is to use frame timing contained within many digital video file's metadata, recorded with 0.000001 sec precision. This paper examines a fatal motor vehicle accident where frame timing information was used with distance measurements from reverse projection photogrammetry to calculate vehicle speed. A margin of error was then calculated based on the accuracy in performing reverse projection photogrammetry distance measurements. The resulting speed calculation was then compared to event data recorder data and found to be within an average of ±1.43538 MPH. Using specific time intervals may lead investigators to more accurate speed calculations, specifically those involving variable frame rate video.
Sea lice loads correlate with the diversity at the Major Histocompatibility Complex ‐related loci in farmed Atlantic salmon, Salmo salar

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Computational study of action potential initiation and action potential backpropagation in mitral cell of the olfactory bulb

A neuron sends information in the form of electrical activity called an action potential. The action potential propagates along the axon to all parts of the cell body. The opposite phenomena of this mechanism were observed in the neurons from various brain area as action potential backpropagation. We studied computationally the action potential initiation and action potential backpropagation in the model of a mitral cell of the olfactory bulb that consists of soma, primary dendrite, secondary dendrite, tuft dendrite, axon hillock, and initial segment. The neuronal activity was constructed with voltage-dependent sodium channels and potassium channels. In the results, we provide that the action potential initiation occurs in soma with an amplitude of 40 mV and the action potential propagation decrease as the distance gets farther from the soma. By plotting the amplitude as a function of the distance from the soma, we obtain the magnitude of action potential backpropagation amplitude has an average of about 42.7 mV. This result consistent with observations in experiments where the normalization of action potential backpropagation amplitude of the mitral cell as a function of the distance from the soma is constant.
“Some of us need to be taken care of”: young adults’ perspectives on support and help in drug reducing interventions in coercive contexts in Denmark and the UK

Abstract This paper provides an account of young people’s experiences of and perspectives on help and support in drug reducing interventions. It is based on interviews with young people age 14–25 who were in contact with the Criminal Justice System (CJS) and, at the same time, participated in a drug reducing intervention. The interview data forms part of the EU funded EPPIC project. Two main themes emerged from the young peoples’ accounts that cut across different types of interventions and social systems in both countries. The first revolves around the ‘system’ of welfare, criminal justice, health and educational services and the barriers young people encountered in navigating the system to find help. The second revolves around the young people’s experiences with professionals, including what they appreciated and what they found problematic in professionals’ approach to them. Basing our analysis on data from two different countries, we are able to emphasize similarities in the young peoples’ perspectives, despite being enrolled in different drug reducing and CJS interventions. The insights gained indicate a need for systems and service changes that can facilitate a better balance between building individual resilience and providing appropriate, timely and adequate support within a ‘resilience-building’ environment.
Cardiac-Specific Cre Induces Age-Dependent Dilated Cardiomyopathy (DCM) in Mice

The genetic modification of the mouse genome using the cre-lox system has been an invaluable tool in deciphering gene and protein function in a temporal and/or spatial manner. However, it has its pitfalls, as researchers have shown that the unregulated expression of cre recombinase can cause DNA damage, the consequences of which can be very detrimental to mouse health. Previously published literature on the most utilized cardiac-specific cre, αMHC-cre, mouse model exhibited a nonlethal hypertrophic cardiomyopathy (HCM) with aging. However, using the same αMHC-cre mice, we observed a cardiac pathology, resulting in complete lethality by 11 months of age. Echocardiography and histology revealed that the αMHC-cre mice were displaying symptoms of dilated cardiomyopathy (DCM) by seven months of age, which ultimately led to their demise in the absence of any HCM at any age. Molecular analysis showed that this phenotype was associated with the DNA damage response through the downregulation of activated p38 and increased expression of JNK, p53, and Bax, known inducers of myocyte death resulting in fibrosis. Our data urges strong caution when interpreting the phenotypic impact of gene responses using αMHC-cre mice, since a lethal DCM was induced by the cre driver in an age-dependent manner in this commonly utilized model system.
Periodicities in the roughness and biofilm growth on glass substrate with etching time: Hydrofluoric acid etchant

Adherence of the microorganism to submerged solid surfaces leads to biofilm formation. Biofilm formation modifies the surfaces in favor of bacteria facilitating the survival of the bacteria under different stressed conditions. On the other hand, the formation of biofilm has a direct adverse economic impact in various industries and more importantly in medical practices. This adherence is the reason for the failure of many indwelling medical devices. Surface biofilm adhesion is the key to biofilm growth and stability. Hence this adhesion needs to be substantially lowered to inhibit biofilm stability. Both chemical and physical properties of the surface influence biofilm formation and modulating these properties can control this formation. In this study, we have investigated the effect of Hydrofluoric acid (HF), at a specific concentration as an etchant, on the surface morphology of substrates and the growth of biofilms of Pseudomonas aeruginosa. and Staphylococcus aureus. We find that the bacterial counts on the etched surfaces undergo a periodic increase and decrease. This, on one hand, shows the close correlation between the biofilm growth and the particular roughness scale, and on the other hand, explains the existing contradictory results regarding the effects of etching on substrate roughness and biofilm growth. We propose a simple model of a sequence of hole formation, hole expansion and etching away of the hole walls to form a new, comparatively smooth surface, coupled with the preferential accumulation of bacteria at the hole edges, to explain these periodicities.
Identification of rfk-1, a Meiotic Driver Undergoing RNA Editing in Neurospora

A Neurospora meiotic drive element known as Spore killer-2 (Sk-2) achieves biased transmission through sexual reproduction by killing siblings that inherit a competing allele. Sk-2 is a meiotic drive element that was discovered in wild populations of Neurospora fungi over 40 years ago. While early studies quickly determined that Sk-2 transmits itself through sexual reproduction in a biased manner via spore killing, the genetic factors responsible for this phenomenon have remained mostly unknown. Here, we identify and characterize rfk-1, a gene required for Sk-2-based spore killing. The rfk-1 gene contains four exons, three introns, and two stop codons, the first of which undergoes RNA editing to a tryptophan codon during sexual development. Translation of an unedited rfk-1 transcript in vegetative tissue is expected to produce a 102-amino acid protein, whereas translation of an edited rfk-1 transcript in sexual tissue is expected to produce a protein with 130 amino acids. These findings indicate that unedited and edited rfk-1 transcripts exist and that these transcripts could have different roles with respect to the mechanism of meiotic drive by spore killing. Regardless of RNA editing, spore killing only succeeds if rfk-1 transcripts avoid silencing caused by a genome defense process called meiotic silencing by unpaired DNA (MSUD). We show that rfk-1’s MSUD avoidance mechanism is linked to the genomic landscape surrounding the rfk-1 gene, which is located near the Sk-2 border on the right arm of chromosome III. In addition to demonstrating that the location of rfk-1 is critical to spore-killing success, our results add to accumulating evidence that MSUD helps protect Neurospora genomes from complex meiotic drive elements.
Low-Risk Effect: Evidence, Explanations and Approaches to Enhancing the Performance of Low-Risk Investment Strategies

The authors offer evidence for low-risk effect from the Indian stock market using the top-500 liquid stocks listed on the National Stock Exchange (NSE) of India for the period from January 2004 to December 2018. Finance theory predicts a positive risk-return relationship. However, empirical studies show that low-risk stocks outperform high-risk stocks on a risk-adjusted basis, and it is called low-risk anomaly or low-risk effect. Persistence of such an anomaly is one of the biggest mysteries in modern finance. The authors find strong evidence in favor of a low-risk effect with a flat (negative) risk-return relationship based on the simple average (compounded) returns. It is documented that low-risk effect is independent of size, value, and momentum effects, and it is robust after controlling for variables like liquidity and ticket-size of stocks. It is further documented that low-risk effect is a combination of stock and sector level effects, and it cannot be captured fully by concentrated sector exposure. By integrating the momentum effect with the low-volatility effect, the performance of a low-risk investment strategy can be improved both in absolute and risk-adjusted terms. The paper contributed to the body of knowledge by offering evidence for: a) robustness of low-risk effect for liquidity and ticket-size of stocks and sector exposure, b) how one can benefit from combining momentum and low-volatility effects to create a long-only investment strategy that offers higher risk-adjusted and absolute returns than plain vanilla, long-only, low-risk investment strategy.
Inhibitor of Apoptosis Proteins Determines Glioblastoma Stem‐Like Cell Fate in an Oxygen‐Dependent Manner

In glioblastomas, apoptosis inhibitor proteins (IAPs) are involved in apoptotic and nonapoptotic processes. We previously showed that IAP inhibition induced a loss of stemness and glioblastoma stem cells differentiation by activating nuclear factor‐κB under normoxic conditions. Hypoxia has been shown to modulate drug efficacy. Here, we investigated how IAPs participate in glioblastoma stem‐like cell maintenance and fate under hypoxia. We showed that in a hypoxic environment, IAPs inhibition by GDC‐0152, a small‐molecule IAPs inhibitor, triggered stem‐like cell apoptosis and decreased proliferation in four human glioblastoma cell lines. We set up a three‐dimensional glioblastoma spheroid model in which time‐of‐flight secondary ion mass spectrometry analyses revealed a decrease in oxygen levels between the periphery and core. We observed low proliferative and apoptotic cells located close to the hypoxic core of the spheres and glial fibrillary acidic protein+ cells at their periphery. These oxygen‐dependent GDC‐0152 antitumoral effects have been confirmed on human glioblastoma explants. Notably, serine–threonine kinase activation analysis revealed that under hypoxic conditions, IAP inhibition activated ataxia telangiectasia and Rad3‐related protein signaling. Our findings provide new insights into the dual mechanism of action of IAP inhibitors that depends on oxygen level and are relevant to their therapeutic application in tumors. Stem Cells 2019;37:731–742
A Pilot Clinical Study on the Prognostic Relevance of Plasmatic Exosomes Levels in Oral Squamous Cell Carcinoma Patients

Background: To evaluate the relationship between the plasmatic CD63 and CAV1 positive exosome levels, in patients with OSCC before and after surgical treatment and to correlate it with their overall survival. Methods: A double-blind pilot study over 10 patients OSCC and T4 stage without distant metastases or local bone invasion has been performed. The average follow-up period was 37.64 months (34.3–40.84). We obtained 2 plasma tubes of 1 mL each before surgery and 7 days after surgery. Before performing the immunocapture-based analysis, EVs (Extracellular Vesicles) were isolated from the plasma and characterized with western blot analysis. Results: Mean values of CD63 positive plasmatic exosomes (EXO-CD63) after surgery decreased from 750.88 ± 286.67 to 541.71 ± 244.93 (p = 0.091). On the other hand, CAV-1 positive plasmatic exosomes (EXO-CAV-1) increased after surgery from 507 ± 483.39 to 1120.25 ± 1151.17 (p = 0.237). Patients with EXO-CD63 levels lower than the mean global value before the surgery had a survival of 36.04 months compared with the group with EXO-CD63 higher than the average who only survived 12.49 ± 1.67 months from the diagnosis, p = 0.225. When EXO-CAV-1 levels before surgery was lower than the average (813.94 ± 801.21) overall survival was 24.69 ± 22.23 months in contrast when it was higher that was only 11.64 months, p = 0.157. Patients with lower EXO-CD63 levels after surgery lived an average of 23.84 ± 23.9 months, while those with higher plasmatic levels of EXO-CD63 live 13.35 months, p = 0.808. When EXO-CAV-1 levels after surgery were lower, the average overall survival was 20.344 ± 15.40 months, in contrast when the EXO-CAV-1 levels were higher showing rather an estimate survival expectation of 1.64 months. Conclusions: Surgical treatment induced a dramatic reduction of the plasmatic levels of exosomes expressing CD63 as early as 1 week after resection. This first result suggests that the tumour mass is responsible of the high levels of circulating exosomes detected in cancer patients. At the same time point exosome expressing CAV-1 increased, possibly due to the inflammatory reaction immediately after surgery. Lastly, statistical analysis showed that lower levels of plasmatic exosomes both before and after surgery correlated with a better life expectancy of OSCC patients. Hopefully, this approach will prove useful in the clinical follow-up of cancer patients.
High Plasma sRAGE (Soluble Receptor for Advanced Glycation End Products) Is Associated With Slower Carotid Intima-Media Thickness Progression and Lower Risk for First-Time Coronary Events and Mortality

Objective— RAGE (receptor for advanced glycation end products) and EMMPRIN (extracellular matrix metalloproteinase inducer) are immune receptors for proinflammatory mediators. These receptors can also be found in a soluble form in the circulation. Soluble RAGE (sRAGE) has shown atheroprotective properties in animal studies, possibly by acting as a decoy receptor for its ligands. Whether sEMMPRIN (soluble EMMPRIN) has similar roles is unknown. We hypothesized that sRAGE and sEMMPRIN might be associated with vascular disease progression, incident coronary events, and mortality. Approach and Results— We measured baseline sRAGE and sEMMPRIN in 4612 cardiovascular disease-free individuals from the population-based Malmö Diet and Cancer cohort. Measurements of intima-media thickness in the common carotid artery were performed at inclusion and after a median of 16.5 years. sRAGE was negatively correlated with carotid intima-media thickness progression, independently of traditional cardiovascular risk factors, kidney function, and hsCRP (high sensitive C-reactive protein). Additionally, sRAGE was associated with decreased risk for major adverse coronary events (hazard ratio=0.90 [0.82–0.97]; P=0.009) and mortality (hazard ratio=0.93 [0.88–0.99]; P=0.011) during a follow-up period of 21 years. The relationship with mortality was independent of all considered potential confounders. We found no correlations between EMMPRIN, intima-media thickness progression, or prognosis. Conclusions— Individuals with high levels of circulating sRAGE have a slower rate of carotid artery disease progression and a better prognosis. Although its predictive value was too weak to promote sRAGE as a useful clinical biomarker in the population, the findings support further research into the potential anti-inflammatory and atheroprotective properties of this soluble receptor.
Executive control in language production by children with and without language impairment.

BACKGROUND Accumulating evidence suggests that the updating, inhibiting and shifting abilities underlying executive control are important for spoken language production in adults. However, little is known about this in children. AIMS To examine whether children with and without language impairment differ in all or only some of these executive abilities, and whether they show corresponding differences when these abilities are engaged in language production. METHODS & PROCEDURES Thirty-three children with specific language impairment (SLI) and 41 typically developing (TD) children (age matched, aged 8-12 years) completed standard executive control tests that measure the updating, inhibiting and shifting abilities. All children were native speakers of Dutch. Moreover, they performed a noun-phrase production task involving picture description within a picture-word interference paradigm. We measured their production accuracy and speed to assess length, distractor and switch effects, which reflect the updating, inhibiting and shifting abilities underlying executive control. OUTCOMES & RESULTS Compared with TD children, the children with SLI had lower scores on all executive control tests. Moreover, they were overall slower and made more errors in the noun-phrase production task. Additionally, the magnitude of the distractor and switch effects was larger for the SLI than for the TD group. CONCLUSIONS & IMPLICATIONS The results suggest that children with SLI have impaired language production and executive control abilities, and that some of the differences in the executive control abilities between SLI and TD groups were reflected in their language production.
Perbandingan Tingkat Pemahaman Mahasiswa STMIK STIKOM Indonesia Pada Metoda Sarrus dan Metoda Cramer pada Penyelesaian Sistem Persamaan Linier

Penelitian ini membahas tentang tingkat pemahaman dari 40 sampel mahasiswa STMIK STIKOM Indonesia pada materi Penyelesaian Sistem Persamaan Linear untuk ordo 3 x 3 menggunakan Eliminasi Gauss dan Aturan Cramer. Prinsip dasar dari kedua metoda tersebut adalah menggunakan operasi matriks. Dari hasil penelitian sebelumnya diperoleh metoda Eliminasi Gauss lebih efektif (langkah penyelesaian dan jumlah operasi aritmatikanya lebih sedikit, serta kecepatan dan ketepatannya lebih baik) dibandingkan Aturan Cramer. Prosedur penelitian ini adalah 40 sampel mahasiswa diberikan satu kasus lalu menyelesaikan dengan kedua metoda tersebut dengan 10 orang memilih metoda Gaussian terlebih dahulu sebagai metoda yang lebih mudah dipahami dan 30 orang sisanya memilih Aturan Cramer. Hal ini menunjukkan bahwa meskipun secara konsep metoda Eliminasi Gauss lebih efektif dibanding dengan Aturan Cramer, tetapi mahasiswa membuktikan lebih memahami Aturan Cramer dibandingkan Eliminasi Gauss. Kata kunci: Eliminasi Gauss; Aturan Cramer; Sisterm Persamaan Linier.
Simultaneous clustering of multiview biomedical data using manifold optimization

MOTIVATION Multiview clustering has attracted much attention in recent years. Several models and algorithms have been proposed for finding the clusters. However, these methods are developed either to find the consistent/common clusters across different views, or to identify the differential clusters among different views. In reality, both consistent and differential clusters may exist in multiview datasets. Thus, development of simultaneous clustering methods such that both the consistent and the differential clusters can be identified is of great importance. RESULTS In this paper, we proposed one method for simultaneous clustering of multiview data based on manifold optimization. The binary optimization model for finding the clusters is relaxed to a real value optimization problem on the Stiefel manifold, which is solved by the line-search algorithm on manifold. We applied the proposed method to both simulation data and four real datasets from TCGA. Both studies show that when the underlying clusters are consistent, our method performs competitive to the state-of-the-art algorithms. When there are differential clusters, our method performs much better. In the real data study, we performed experiments on cancer stratification and differential cluster (module) identification across multiple cancer subtypes. For the patients of different subtypes, both consistent clusters and differential clusters are identified at the same time. The proposed method identifies more clusters that are enriched by gene ontology and KEGG pathways. The differential clusters could be used to explain the different mechanisms for the cancer development in the patients of different subtypes. SUPPLEMENTARY INFORMATION Codes can be downloaded from: http://homepage.fudan. edu.cn/sqzhang/files/2018/12/MVCMOcode.zip. Supplementary data are available upon request.