Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of biopsy on the MRI radiomics classification of benign lesions and luminal A cancers

Radiomic features extracted from breast magnetic resonance (MR) images have demonstrated potential in diagnosis and prognosis of breast cancer. However, presentation of lesions on MRI may be affected by a biopsy event. We investigated, relative to biopsy condition, the difference in radiomic features and performance (the area under the receiver operating curve (AUC)) for the task of distinguishing between benign lesions and luminal A cancers. Dynamic contrast-enhanced MR images were collected retrospectively under IRB/HIPAA compliance. The 361-case dataset included 92 benign and 30 luminal A lesions imaged pre-biopsy and 40 benign and 199 luminal A lesions imaged post-biopsy. Thirty-four radiomic non-size features were extracted and their values compared for each group of lesions by biopsy condition using the Kolmogorov-Smirnov test to determine if the two groups were drawn from the same patient distribution. For each feature by biopsy condition, the median of the AUC and the confidence interval for the difference in AUC were determined (2000 bootstrap iterations). In all analyses, after correction for multiple comparisons, a difference was considered significant when the p-value was less than 0.0015 (0.05/34) or, equivalently, the 99.85% confidence interval for the difference excluded zero. If comparisons failed to meet p < 0.0015, features were considered potentially robust. While, as expected, the morphology feature of irregularity was significantly different (p = 0.0003) for benign lesions due to how biopsy events increased irregularity of benign lesions, most features were potentially robust between biopsy conditions. While features did well in distinguishing between luminal A and benign lesions, all failed to demonstrate significance differences in AUC between biopsy conditions.
Alanine, a Novel Growth Substrate for the Acetogenic Bacterium Acetobacterium woodii

Peptides and amino acids are widespread in nature, but there are only a few reports that demonstrated use of amino acids as carbon and energy sources by acetogenic bacteria, a central and important group in the anaerobic food web. Our finding that A. woodii can perform alanine oxidation coupled to reduction of carbon dioxide not only increases the number of substrates that can be used by this model acetogen but also raises the possibility that other acetogens may also be able to use alanine. Indeed, the alanine genes are also present in at least two more acetogens, for which growth on alanine has not been reported so far. Alanine may be a promising substrate for industrial fermentations, since acid formation goes along with the production of a base (NH3) and pH regulation is a minor issue. ABSTRACT Acetogenic bacteria are an ecophysiologically important group of strictly anaerobic bacteria that grow lithotrophically on H2 plus CO2 or on CO or heterotrophically on different substrates such as sugars, alcohols, aldehydes, or acids. Amino acids are rarely used. Here, we describe that the model acetogen Acetobacterium woodii can use alanine as the sole carbon and energy source, which is in contrast to the description of the type strain. The alanine degradation genes have been identified and characterized. A key to alanine degradation is an alanine dehydrogenase which has been characterized biochemically. The resulting pyruvate is further degraded to acetate by the known pathways involving the Wood-Ljungdahl pathway. Our studies culminate in a metabolic and bioenergetic scheme for alanine-dependent acetogenesis in A. woodii. IMPORTANCE Peptides and amino acids are widespread in nature, but there are only a few reports that demonstrated use of amino acids as carbon and energy sources by acetogenic bacteria, a central and important group in the anaerobic food web. Our finding that A. woodii can perform alanine oxidation coupled to reduction of carbon dioxide not only increases the number of substrates that can be used by this model acetogen but also raises the possibility that other acetogens may also be able to use alanine. Indeed, the alanine genes are also present in at least two more acetogens, for which growth on alanine has not been reported so far. Alanine may be a promising substrate for industrial fermentations, since acid formation goes along with the production of a base (NH3) and pH regulation is a minor issue.
Measuring Surface Water Quality Using a Low-Cost Sensor Kit within the Context of Rural Africa

Monitoring water quality is done for a variety of reasons, including to determine whether water is suitable for drinking or agricultural purposes. In rural areas of Africa the traditional way of measuring water quality can be costly and time consuming. In this research, we have developed a low-cost water quality measuring device that designed to operate in the context of rural Africa. Firstly we select appropriate water quality sensors. Secondly we developed a water quality monitoring device that takes the contextual requirements and constraints of rural Africa into account. Lastly the device is evaluated and tested using water samples that were collected in rural Africa.
The Role of Tumor Microenvironment in Chemoresistance: 3D Extracellular Matrices as Accomplices

Background: The functional interplay between tumor cells and their adjacent stroma has been suggested to play crucial roles in the initiation and progression of tumors and the effectiveness of chemotherapy. The extracellular matrix (ECM), a complex network of extracellular proteins, provides both physical and chemicals cues necessary for cell proliferation, survival, and migration. Understanding how ECM composition and biomechanical properties affect cancer progression and response to chemotherapeutic drugs is vital to the development of targeted treatments. Methods: 3D cell-derived-ECMs and esophageal cancer cell lines were used as a model to investigate the effect of ECM proteins on esophageal cancer cell lines response to chemotherapeutics. Immunohistochemical and qRT-PCR evaluation of ECM proteins and integrin gene expression was done on clinical esophageal squamous cell carcinoma biopsies. Esophageal cancer cell lines (WHCO1, WHCO5, WHCO6, KYSE180, KYSE 450 and KYSE 520) were cultured on decellularised ECMs (fibroblasts-derived ECM; cancer cell-derived ECM; combinatorial-ECM) and treated with 0.1% Dimethyl sulfoxide (DMSO), 4.2 µM cisplatin, 3.5 µM 5-fluorouracil and 2.5 µM epirubicin for 24 h. Cell proliferation, cell cycle progression, colony formation, apoptosis, migration and activation of signaling pathways were used as our study endpoints. Results: The expression of collagens, fibronectin and laminins was significantly increased in esophageal squamous cell carcinomas (ESCC) tumor samples compared to the corresponding normal tissue. Decellularised ECMs abrogated the effect of drugs on cancer cell cycling, proliferation and reduced drug induced apoptosis by 20–60% that of those plated on plastic. The mitogen-activated protein kinase-extracellular signal-regulated kinase (MEK-ERK) and phosphoinositide 3-kinase-protein kinase B (PI3K/Akt) signaling pathways were upregulated in the presence of the ECMs. Furthermore, our data show that concomitant addition of chemotherapeutic drugs and the use of collagen- and fibronectin-deficient ECMs through siRNA inhibition synergistically increased cancer cell sensitivity to drugs by 30–50%, and reduced colony formation and cancer cell migration. Conclusion: Our study shows that ECM proteins play a key role in the response of cancer cells to chemotherapy and suggest that targeting ECM proteins can be an effective therapeutic strategy against chemoresistant tumors.
The Microbiome and Tuberculosis: Early Evidence for Cross Talk

Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied both clinically and experimentally. Although susceptibility to Mycobacterium tuberculosis infection is clearly influenced by factors such as nutrition, immune status, and both mycobacterial and host genetics, the variable pathogenesis of TB in infected individuals remains poorly understood. ABSTRACT Tuberculosis (TB) is an ancient infectious disease of humans that has been extensively studied both clinically and experimentally. Although susceptibility to Mycobacterium tuberculosis infection is clearly influenced by factors such as nutrition, immune status, and both mycobacterial and host genetics, the variable pathogenesis of TB in infected individuals remains poorly understood. During the past two decades, it has become clear that the microbiota—the trillion organisms that reside at mucosal surfaces within and on the body—can exert a major influence on disease outcome through its effects on host innate and adaptive immune function and metabolism. This new recognition of the potentially pleiotropic participation of the microbiome in immune responses has raised the possibility that the microbiota may influence M. tuberculosis infection and/or disease. Similarly, treatment of TB may alter the healthy steady-state composition and function of the microbiome, possibly affecting treatment outcome in addition to other host physiological parameters. Herein, we review emerging evidence for how the microbiota may influence the transition points in the life cycle of TB infection, including (i) resistance to initial infection, (ii) initial infection to latent tuberculosis (LTBI), (iii) LTBI to reactivated disease, and (iv) treatment to cure. A major goal of this review is to frame questions to guide future scientific and clinical studies in this largely unexplored but increasingly important area of TB research.
Comparative in vivo constituents and pharmacokinetic study in rats after oral administration of ultrafine granular powder and traditional decoction slices of Chinese Salvia.

Salvia miltiorrhiza, one of the most well-known herbal medicines, is commonly used for the treatment of coronary heart diseases in China. Besides traditional decoction slices (TDS), another relatively new product of S. miltiorrhiza, ultrafine granular powder (UGP; D90 < 45 μm), is also increasingly being used. In this paper, a UHPLC-LTQ-Orbitrap MS technique was developed for a metabolite profile study after oral administration of UGP and TDS of S. miltiorrhiza. The results showed that the number of in vivo absorbed compounds from UGP was much greater than that from TDS, and different types of products from S. miltiorrhiza will have different metabolic processes in vivo. Furthermore, a UHPLC-Q-Trap MS/MS method for simultaneously determining four tanshinones (tanshinone IIA, dihydrotanshinone I, tanshinone I and cryptotanshinone) was established and applied to assess the pharmacokinetics of the two types of products. All of the analytes displayed significant higher area under the concentration-time curve and peak concentration after oral administration of UGP than after TDS, indicating that ultrafine powder product could improve the bioavailability and absorption of cryptotanshinon,tanshinone II A,dihydrotanshinonE I and tanshinone I in vivo. The present study provides scientific information for further exploration of the pharmacology of these two types of S. miltiorrhiza and offers a reference for clinical administration of S. miltiorrhiza.
3D Photography

Over the last decade, digital photography has entered the mainstream with inexpensive, miniaturized cameras for consumer use. Digital projection is poised to make a similar breakthrough. In particular, low-cost homemade 3D scanners are now within reach. This book gives beginners the necessary mathematics, software, and practical details to leverage projector-camera systems in their own 3D scanning projects. Featuring an example-driven approach, the text illustrates each new concept using a practical scanner implemented with off-the-shelf parts. It shows how these new approaches are used in rapid prototyping, entertainment, cultural heritage, and web-based applications.
Fatal Toxic Effects Associated With Immune Checkpoint Inhibitors: A Systematic Review and Meta-analysis

Importance Immune checkpoint inhibitors (ICIs) are now a mainstay of cancer treatment. Although rare, fulminant and fatal toxic effects may complicate these otherwise transformative therapies; characterizing these events requires integration of global data. Objective To determine the spectrum, timing, and clinical features of fatal ICI-associated toxic effects. Design, Setting, and Participants We retrospectively queried a World Health Organization (WHO) pharmacovigilance database (Vigilyze) comprising more than 16 000 000 adverse drug reactions, and records from 7 academic centers. We performed a meta-analysis of published trials of anti–programmed death-1/ligand-1 (PD-1/PD-L1) and anti–cytotoxic T lymphocyte antigen-4 (CTLA-4) to evaluate their incidence using data from large academic medical centers, global WHO pharmacovigilance data, and all published ICI clinical trials of patients with cancer treated with ICIs internationally. Exposures Anti–CTLA-4 (ipilimumab or tremelimumab), anti–PD-1 (nivolumab, pembrolizumab), or anti–PD-L1 (atezolizumab, avelumab, durvalumab). Main Outcomes and Measures Timing, spectrum, outcomes, and incidence of ICI-associated toxic effects. Results Internationally, 613 fatal ICI toxic events were reported from 2009 through January 2018 in Vigilyze. The spectrum differed widely between regimens: in a total of 193 anti–CTLA-4 deaths, most were usually from colitis (135 [70%]), whereas anti–PD-1/PD-L1–related fatalities were often from pneumonitis (333 [35%]), hepatitis (115 [22%]), and neurotoxic effects (50 [15%]). Combination PD-1/CTLA-4 deaths were frequently from colitis (32 [37%]) and myocarditis (22 [25%]). Fatal toxic effects typically occurred early after therapy initiation for combination therapy, anti–PD-1, and ipilimumab monotherapy (median 14.5, 40, and 40 days, respectively). Myocarditis had the highest fatality rate (52 [39.7%] of 131 reported cases), whereas endocrine events and colitis had only 2% to 5% reported fatalities; 10% to 17% of other organ-system toxic effects reported had fatal outcomes. Retrospective review of 3545 patients treated with ICIs from 7 academic centers revealed 0.6% fatality rates; cardiac and neurologic events were especially prominent (43%). Median time from symptom onset to death was 32 days. A meta-analysis of 112 trials involving 19 217 patients showed toxicity-related fatality rates of 0.36% (anti–PD-1), 0.38% (anti–PD-L1), 1.08% (anti–CTLA-4), and 1.23% (PD-1/PD-L1 plus CTLA-4). Conclusions and Relevance In the largest evaluation of fatal ICI-associated toxic effects published to date to our knowledge, we observed early onset of death with varied causes and frequencies depending on therapeutic regimen. Clinicians across disciplines should be aware of these uncommon lethal complications.
Phase‐locked responses to the vowel envelope vary in scalp‐recorded amplitude due to across‐frequency response interactions

Neural encoding of the envelope of sounds like vowels is essential to access temporal information useful for speech recognition. Subcortical responses to envelope periodicity of vowels can be assessed using scalp‐recorded envelope following responses (EFRs); however, the amplitude of EFRs vary by vowel spectra and the causal relationship is not well understood. One cause for spectral dependency could be interactions between responses with different phases, initiated by multiple stimulus frequencies. Phase differences can arise from earlier initiation of processing high frequencies relative to low frequencies in the cochlea. This study investigated the presence of such phase interactions by measuring EFRs to two naturally spoken vowels (/ε/ and /u/), while delaying the envelope phase of the second formant band (F2+) relative to the first formant (F1) band in 45° increments. At 0° F2+ phase delay, EFRs elicited by the vowel /ε/ were lower in amplitude than the EFRs elicited by /u/. Using vector computations, we found that the lower amplitude of /ε/‐EFRs was caused by linear superposition of F1‐ and F2+‐contributions with larger F1‐F2+ phase differences (166°) compared to /u/ (19°). While the variation in amplitude across F2+ phase delays could be modeled with two dominant EFR sources for both vowels, the degree of variation was dependent on F1 and F2+ EFR characteristics. Together, we demonstrate that (a) broadband sounds like vowels elicit independent responses from different stimulus frequencies that may be out‐of‐phase and affect scalp‐based measurements, and (b) delaying higher frequency formants can maximize EFR amplitudes for some vowels.
Uma Abordagem Baseada em Aprendizagem de Máquina para Predição de Falhas de Revogação em Instâncias Transientes

Cloud computing providers has started offering their idle resources as transient servers. Spot instances are transient servers offered by Amazon, having their prices dynamically changed over time based on supply and demand. Using an appropriate strategic and fault tolerance mechanisms, users can effectively use spot instances to run applications in a lower price. This paper presents a strategy that combines both machine learning and a statistical model to predict time to instance revocation. Our experiments demonstrate that our heuristic is able to predict with high levels of accuracy. We evaluate our strategy and our results achieve 94% of success, which show that our model are effective and reaches high levels of accuracy under realistic working conditions. Resumo. Computação em nuvem oferece seus recursos ociosos através de servidores transientes. Estes servidores são oferecidos pela Amazon como instâncias spots, que varia o seu preço de acordo com a oferta e procura. Utilizando mecanismos de tolerância a falhas e estratégias apropriadas, usuários podem executar aplicações nestas instâncias e diminuir o seu custo. Este artigo apresenta a combinação de aprendizagem de máquina e um modelo estatı́stico na predição do tempo até a sua revogação. Exaustivos experimentos demonstraram que a estratégia proposta atinge altos nı́veis de acurácia em sua predição. Com resultados que alcançam 94% de sucesso, nossa estratégia mostra a sua eficiência quando submetida a condições reais de uso dessas instâncias spots.
Cell Wall Glycans Mediate Recognition of the Dairy Bacterium Streptococcus thermophilus by Bacteriophages

Streptococcus thermophilus is widely used in starter cultures for cheese and yoghurt production. During dairy fermentations, infections of bacteria with bacteriophages result in acidification failures and a lower quality of the final products. An understanding of the molecular factors involved in phage-host interactions, in particular, the phage receptors in dairy bacteria, is a crucial step for developing better strategies to prevent phage infections in dairy plants. ABSTRACT Receptors on the cell surfaces of bacterial hosts are essential during the infection cycle of bacteriophages. To date, the phage receptors of the industrial relevant dairy starter bacterium Streptococcus thermophilus remain elusive. Thus, we set out to identify cell surface structures that are involved in host recognition by dairy streptococcal phages. Five industrial S. thermophilus strains sensitive to different phages (pac type, cos type, and the new type 987), were selected to generate spontaneous bacteriophage-insensitive mutants (BIMs). Of these, approximately 50% were deselected as clustered regularly interspaced short palindromic repeat (CRISPR) mutants, while the other pool was further characterized to identify receptor mutants. On the basis of genome sequencing data, phage resistance in putative receptor mutants was attributed to nucleotide changes in genes encoding glycan biosynthetic pathways. Superresolution structured illumination microscopy was used to visualize the interactions between S. thermophilus and its phages. The phages were either regularly distributed along the cells or located at division sites of the cells. The cell wall structures mediating the latter type of phage adherence were further analyzed via phenotypic and biochemical assays. Altogether, our data suggested that phage adsorption to S. thermophilus is mediated by glycans associated with the bacterial cell surface. Specifically, the pac-type phage CHPC951 adsorbed to polysaccharides anchored to peptidoglycan, while the 987-type phage CHPC926 recognized exocellular polysaccharides associated with the cell surface. IMPORTANCE Streptococcus thermophilus is widely used in starter cultures for cheese and yoghurt production. During dairy fermentations, infections of bacteria with bacteriophages result in acidification failures and a lower quality of the final products. An understanding of the molecular factors involved in phage-host interactions, in particular, the phage receptors in dairy bacteria, is a crucial step for developing better strategies to prevent phage infections in dairy plants.
Do powered over-ground lower limb robotic exoskeletons affect outcomes in the rehabilitation of people with acquired brain injury?

Abstract Purpose: To assess the effects of lower limb robotic exoskeletons on outcomes in the rehabilitation of people with acquired brain injury. Materials and methods: A systematic review of seven electronic databases was conducted. The primary outcome of interest was neuromuscular function. Secondary outcomes included quality of life, mood, acceptability and safety. Studies were assessed for methodological quality and recommendations were made using the GRADE system. Results: Of 2469 identified studies, 13 (n = 322) were included in the review. Five contained data suitable for meta-analysis. When the data were pooled, there were no differences between exoskeleton and control for 6-Minute Walk Test, Timed Up and Go or 10-Meter Walk Test. Berg Balance Scale outcomes were significantly better in controls (MD = 2.74, CI = 1.12–4.36, p = 0.0009). There were no severe adverse events but drop-outs were 11.5% (n = 37). No studies reported the effect of robotic therapy on quality of life or mood. Methodological quality was on average fair (15.6/27 on Downs and Black Scale). Conclusions: Only small numbers of people with acquired brain injury had data suitable for analysis. The available data suggests no more benefit for gait or balance with robotic therapy than conventional therapy. However, some important outcomes have not been studied and further well-conducted research is needed to determine whether such devices offer benefit over conventional therapy, in particular subgroups of those with acquired brain injury. Implications for Rehabilitation There is adequate evidence to recommend that powered over-ground lower limb robotic exoskeletons should not be used clinically in those with ABI, and that use should be restricted to research. Further research (controlled trials) with dependent ambulators is recommended. Research of other outcomes such as acceptability, spasticity, sitting posture, cardiorespiratory and psychological function, should be considered.