Miracle-dz/UniFAR-FTUs huggingface dataset:
Eikelboom filamentous morphotypes 0675 and 0041 embrace members of the Chloroflexi: resolving their phylogeny, and design of fluorescence in situ hybridisation probes for their identification

ABSTRACT Although the phylogeny of many of the filamentous bacteria responsible for bulking in activated sludge plants is now known, and fluorescence in situ hybridisation (FISH) probes have been designed for their in situ identification, there are some noticeable exceptions. This study reports the identification of the Eikelboom morphotypes 0041 and 0675. Because these morphotypes differ only in their filament diameters, they are often considered together in surveys based on microscopic identifications. Here we show that they are phylogenetically distinct, and so should be viewed no longer as morphological variants of a single population. Amplicon sequencing data of Australian EBPR plant biomass containing types 0041 and 0675, and phylogenetic analysis have revealed that both, like many other bulking filament morphotypes, are members of the phylum Chloroflexi and probably representatives of two different genera. FISH probes are described here targeting each. Surveys carried out on Australian activated sludge plants suggest that type 0675 occurs more in plants designed to remove phosphorus, while type 0041 shows no such preference, and was seen in biomass samples from a wide range of plant configurations.
Prevalence of Human Papillomavirus in Elderly Women with Cervical Cancer

To investigate the relation between the prevalence of human papillomavirus (HPV) and age in cervical cancer patients, material from 93 patients with Ia–IIb cervical carcinoma was analyzed for the presence of HPV by both type-specific and general primer polymerase chain reaction. Patients were divided into 2 groups: 64 years or younger, and 65 years and older. There was no statistically significant difference in either the prevalence of HPV DNA or distribution of genotypes amongst the 2 groups. Therefore, HPV detection can be equally well used in the management and follow-up of elderly cervical cancer patients.
Automation , Human Capital and Welfare : The Stochastic Uzawa-Lucas Approach

Human capital, in the form of embodied knowledge or skills, is under threat of automation. To examine the effect of it on a macroeconomy, I develop the Uzawa-Lucas model in which the accumulation of human capital follows the stochastic process. With two equality constraints, the closed-form solution gets obtainable. It shows that increase in uncertainty about the human capital accumulation reduces the welfare of households and causes human capital contraction. Moreover, optimal consumption appears to depend on efficiency of human capital, not its stock.
Gently Does It: Humans Outperform a Software Classifier in Recognizing Subtle, Nonstereotypical Facial Expressions

According to dominant theories of affect, humans innately and universally express a set of emotions using specific configurations of prototypical facial activity. Accordingly, thousands of studies have tested emotion recognition using sets of highly intense and stereotypical facial expressions, yet their incidence in real life is virtually unknown. In fact, a commonplace experience is that emotions are expressed in subtle and nonprototypical forms. Such facial expressions are at the focus of the current study. In Experiment 1, we present the development and validation of a novel stimulus set consisting of dynamic and subtle emotional facial displays conveyed without constraining expressers to using prototypical configurations. Although these subtle expressions were more challenging to recognize than prototypical dynamic expressions, they were still well recognized by human raters, and perhaps most importantly, they were rated as more ecological and naturalistic than the prototypical expressions. In Experiment 2, we examined the characteristics of subtle versus prototypical expressions by subjecting them to a software classifier, which used prototypical basic emotion criteria. Although the software was highly successful at classifying prototypical expressions, it performed very poorly at classifying the subtle expressions. Further validation was obtained from human expert face coders: Subtle stimuli did not contain many of the key facial movements present in prototypical expressions. Together, these findings suggest that emotions may be successfully conveyed to human viewers using subtle nonprototypical expressions. Although classic prototypical facial expressions are well recognized, they appear less naturalistic and may not capture the richness of everyday emotional communication.
Thalamo‐cortical projections to the macaque superior parietal lobule areas PEc and PE

The exposed surface of the superior parietal lobule in macaque brain contains two architectonically defined areas named PEc and PE. The aim of the present study is the characterization of thalamic afferents of these two areas. For this purpose, retrograde neuronal tracers were injected, or placed in crystal form, in areas PEc and PE. We found that the two areas show a similar pattern of thalamic inputs, mainly originating from Lateral Posterior (LP), Pulvinar (Pul), Ventral Posterior Lateral (VPL), and Ventral Lateral (VL) nuclei, all structures known to be involved in visual, somatosensory, and/or sensorimotor processing. Minor afferents were observed from the Centromedian/Parafascicular complex (CM/PF), Central Lateral (CL), Ventral Anterior (VA), and Medial Dorsal (MD) nuclei. LP and VL were more strongly connected to PEc than to PE, while the other main thalamic inputs to the two areas showed slight differences in strength. The part of the Pul mostly connected with areas PEc and PE was the Medial Pul. No labeled cells were found in the retinotopically organized Lateral and Inferior Pul. In the somatotopically organized VPL and VL nuclei, labeled neurons were mainly found in regions likely to correspond to the trunk and limb representations (in particular the legs). These findings are in line with the sensory‐motor nature of areas PEc and PE, and with their putative functional roles, being them suggested to be involved in the preparation and control of limb interaction with the environment, and in locomotion.
Diet quality and academic achievement – A prospective study among primary school children

1 Purpose: Poor diet quality may impair academic achievement in children, but such evidence is 2 limited. Therefore, we investigated the associations of healthy diet in Grade 1 assessed by 3 Mediterranean Diet Score (MDS), Baltic Sea Diet Score (BSDS), and Finnish Children Healthy 4 Eating Index (FCHEI) with academic achievement in Grades 1–3 in children. 5 Methods: The participants were 161 Finnish children who were 6–8-year-old in Grade 1 and 6 attended in a large ongoing physical activity and dietary intervention study. Dietary factors were 7 assessed using 4-day food records and MDS, BSDS, and FCHEI were calculated. Academic 8 achievement was assessed by reading fluency, reading comprehension, and arithmetic skill tests. 9 The data were analyzed using linear regression analysis and analysis of covariance adjusted for age, 10 sex, parental education, household income, body fat percentage, physical activity, the PANIC Study 11 group, and total energy intake. 12 Results: MDS was positively associated with reading comprehension in Grade 3 (standardized 13 regression coefficient β =0.167, P =0.032). BSDS was positively associated with reading fluency in 14 Grades 2–3 and reading comprehension in Grades 1–3 ( β =0.161 to 0.274, P <0.05). FCHEI was 15 positively related to reading fluency in Grades 1–2 and reading comprehension in Grades 1–3 16 ( β =0.190 to 0.344, P <0.05). Children in the highest third of BSDS and FCHEI had better reading 17 fluency and reading comprehension in Grades 1–3 than children in the lowest third ( P <0.05). None 18 of the diet scores was associated with arithmetic skills. 19 Conclusions: Healthier diet assessed by BSDS or FCHEI in Grade 1 was associated with better 20 reading skills, but not with arithmetic skills, among children in Grades 1–3. Long-term intervention 21 studies are needed to investigate the effects of improvements in diet quality on academic
New and emerging therapies for acute and chronic graft versus host disease

Graft versus host disease (GVHD) remains a major cause of morbidity and mortality following allogeneic hematopoietic stem-cell transplantation (HSCT). Despite the use of prophylactic GVHD regimens, a significant proportion of transplant recipients will develop acute or chronic GVHD following HSCT. Corticosteroids are standard first-line therapy, but are only effective in roughly half of all cases with ~50% of patients going on to develop steroid-refractory disease, which increases the risk of nonrelapse mortality. While progress has been made with improvements in survival outcomes over time, corticosteroids are associated with significant toxicities, and many currently available salvage therapies are associated with increased immunosuppression, infectious complications, and potential loss of the graft versus leukemia (GVL) effect. Thus, there is an unmet need for development of newer treatment strategies for both acute and chronic GVHD to improve long-term post-transplant outcomes and quality of life for HSCT recipients. Here, we provide a concise review of major emerging therapies currently being studied in the treatment of acute and chronic GVHD.
STAT3 potentiates the ability of airway smooth muscle cells to promote angiogenesis by regulating VEGF signalling

What is the central question of this study? Airway angiogenesis occurs in asthma, and airway smooth muscle (ASM) cells have been reported to be capable of promoting airway angiogenesis. What is the potential mechanism by which ASM cells harvested from patients with asthma are capable of promoting airway angiogenesis? What is the main finding and its importance? Endogenous STAT3 mediated the pro‐angiogenic ability of ASM cells by directly activating VEGF signalling. These findings contribute to the understanding of airway angiogenesis in pathology and could represent a possible therapeutic target for asthma.
Obese children aged 4–6 displayed decreased fasting and postprandial ghrelin levels in response to a test meal

Ghrelin is a hunger hormone that plays a role in glucose homoeostasis and its levels increase before a meal and decrease during and after eating. This study compared the fasting ghrelin and insulin levels of obese children aged 4–6 with those of normal weight children and tested postprandial ghrelin levels in the obese children after a standard breakfast.
Machine learning in autistic spectrum disorder behavioral research: A review and ways forward

ABSTRACT Autistic Spectrum Disorder (ASD) is a mental disorder that retards acquisition of linguistic, communication, cognitive, and social skills and abilities. Despite being diagnosed with ASD, some individuals exhibit outstanding scholastic, non-academic, and artistic capabilities, in such cases posing a challenging task for scientists to provide answers. In the last few years, ASD has been investigated by social and computational intelligence scientists utilizing advanced technologies such as machine learning to improve diagnostic timing, precision, and quality. Machine learning is a multidisciplinary research topic that employs intelligent techniques to discover useful concealed patterns, which are utilized in prediction to improve decision making. Machine learning techniques such as support vector machines, decision trees, logistic regressions, and others, have been applied to datasets related to autism in order to construct predictive models. These models claim to enhance the ability of clinicians to provide robust diagnoses and prognoses of ASD. However, studies concerning the use of machine learning in ASD diagnosis and treatment suffer from conceptual, implementation, and data issues such as the way diagnostic codes are used, the type of feature selection employed, the evaluation measures chosen, and class imbalances in data among others. A more serious claim in recent studies is the development of a new method for ASD diagnoses based on machine learning. This article critically analyses these recent investigative studies on autism, not only articulating the aforementioned issues in these studies but also recommending paths forward that enhance machine learning use in ASD with respect to conceptualization, implementation, and data. Future studies concerning machine learning in autism research are greatly benefitted by such proposals.
Physiologic Evaluation of 4 Weeks of Nocturnal Nasal Positive Pressure Ventilation in Stable Hypercapnic Patients with Chronic Obstructive Pulmonary Disease

Background: The long-term daily use of noninvasive mechanical ventilation (NIMV) to treat chronic respiratory failure in chronic obstructive pulmonary disease (COPD) patients is not widely recommended, partly because of a lack of clear clinical results and partly because the physiological mechanisms by which the daily application of NIMV would be helpful in these patients have not yet been clarified. Objectives: We designed a physiological study in order to assess the effects of supervised long-term NIMV on gas exchange, respiratory muscle function, pulmonary mechanics and to ascertain the possible effect of the treatment in responders and nonresponders. Methods: Fourteen consecutive inpatients with stable hypercapnic COPD (pH = 7.37 ± 0.01; PaCO2 = 56.73 ± 6.48 mm Hg) underwent 4 weeks of nocturnal NIMV delivered with a bilevel ventilator ‘physiologically’ set to reduce tidal transdiaphragmatic pressure (Pdi) by at least 50% and the amount of dynamic intrinsic positive end-expiratory pressure by 70%. Various measurements were compared with those obtained in a control group of consecutive patients with comparable baseline characteristics who refused NIMV and underwent breathing exercises for the same period of time. Results: By the end of the 4 weeks NIMV had induced a slight but significant (p < 0.01) reduction in resting PaCO2 (53.78 ± 5.64 mm Hg) associated with a decrease in the pressure time product of the diaphragm per minute (from 172 ± 60 to 136 ± 61 cm H2O/l/s; p < 0.05). This latter value was primarily due to a significant shortening of the inspiratory duty cycle, while Pdi and lung mechanics were not modified. Eight of the 13 NIMV-treated patients (1 dropped out for nonmedical reasons) had a clear reduction in PaCO2 (>3 mm Hg or >5% from enrollment) and were classified as responders. The acute reduction in PaCO2 during the first trial with NIMV resulted to be a strong index of the final response. The subgroup of responders had a significantly increased maximal Pdi (from 41 ± 19 to 49 ± 23 cm H2O, p < 0.05) and an enhanced ability of the ventilatory pump to clear CO2 (9.7 ± 3.4 vs. 7.2 ± 2.9 cm H2O × s/min; p < 0.01). No significant changes were observed in the control group. Conclusions: These results suggest that in a remarkable and identifyable proportion of patients with stable hypercapnic COPD, nocturnal NIMV may decrease resting PaCO2, reraising the role of chronically supporting the respiratory pump.
The complete mitochondrial genome of the orange-spotted grouper Epinephelus coioides (Perciformes, Serranidae)

Abstract We present the complete mitochondrial genome of Epinephelus coioides in this study. The mitochondrial genome is 16,458 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. All of them are encoded on the heavy strand except ND6 and 8 tRNA genes on the light strand. The nucleotide compositions of the light strand are 28.88% of G, 28.75% of T, 26.58% of A and 15.80% of C. All the protein-coding genes share ATG initiation codon except ATP6 with CTG and COXI with GTG, and four types of inferred termination codons are T (ND2, COXII, ND3, ND4 and Cytb), TA (COXIII), TAA (ND1, ATP8, ND4L, ND5, ATP6 and COXI) and TAG (ND6). There are 10 intergenic spacers, 5 gene overlaps and no tandem repeat sequence. Gene arrangement and distribution are consistent with the typical vertebrates.
Bone loss at implants and teeth in the same inter‐proximal unit: A radiographic study

OBJECTIVE This study was performed to determine whether the distance between an implant and a tooth present in an inter-proximal unit influenced the amount of marginal bone loss that occurred at the two facing (adjacent) surfaces. MATERIALS AND METHODS One hundred and eighty patients with a total of 278 inter-proximal units were included. Radiographs of implants that also included adjacent (facing) natural tooth/teeth were digitalized, and various linear measurements were performed using a software program. The marginal bone level and the bone level change that had occurred during a mean of 5.8 years were assessed as well as distance between the implant and the adjacent tooth/teeth. RESULTS The mean amount of additional marginal bone loss that took place during the observation period was about 0.4 mm at both implants and adjacent tooth surfaces. The horizontal distance between an implant and the facing tooth did not influence the amount of marginal bone loss that had occurred. In most inter-proximal units, more advanced bone loss (>1 mm, >2 mm) had ensued either at the implant or at the facing tooth surface. Advanced additional bone loss occurred at both the implant and the tooth in only about 3% of the examined subjects. CONCLUSION Bone loss at implants and teeth appears to be a site-specific phenomenon and not dependent on the inter-proximal distance.
Extended Treatment with Single-Agent Ibrutinib at the 420 mg Dose Leads to Durable Responses in Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma

Purpose: Ibrutinib, a first-in-class, once-daily, oral inhibitor of Bruton tyrosine kinase, promotes apoptosis, and inhibits B-cell proliferation, adhesion, and migration. Ibrutinib has demonstrated single-agent efficacy and acceptable tolerability at doses of 420 and 840 mg in patients with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) who were treatment-naïve (TN) or had relapsed/refractory (R/R) CLL after ≥1 prior therapy in a phase Ib/II study (PCYC-1102). Subsequently, the ibrutinib 420 mg dose was approved in CLL. Experimental Design: We report data with 44 months of follow-up on 94 patients with TN and R/R CLL/SLL receiving ibrutinib 420 mg once-daily in PCYC-1102 and the long-term extension study PCYC-1103. Results: Ninety-four CLL/SLL patients (27 TN, 67 R/R) were treated with ibrutinib (420 mg/day). Patients with R/R disease had received a median of four prior therapies (range, 1–12). Responses were rapid and durable and median duration of response was not reached. Best overall response was 91% [85% TN (complete response, CR 26%) and 94% R/R (9% CR)]. Median progression-free survival (PFS) was not reached in either group. The 30-month PFS rate was 96% and 76% for TN and R/R patients, respectively. Ibrutinib was well tolerated with extended follow-up; rates of grade ≥3 cytopenias and fatigue, as well as discontinuations due to toxicities decreased over time. Conclusions: Single-agent ibrutinib at 420 mg once-daily resulted in durable responses and was well tolerated with up to 44 months follow-up in patients with TN and R/R CLL/SLL. Currently, 66% of patients continue on ibrutinib. Clin Cancer Res; 23(5); 1149–55. ©2017 AACR.
Effectiveness and confounding factors of penetrating astigmatic keratotomy in clinical practice

Rationale: Penetrating astigmatic keratotomy (penetrating AK) is a well-known method to correct corneal astigmatism but rarely be performed nowadays. This article reevaluated the clinical effectiveness and confounding factors of penetrating AK. Patient concerns: Penetrating AK has been introduced to serve as one alternative operation for astigmatism correction, and is thought to have the potential advantage of being more affordable and easy to perform. The purpose of our study is to evaluate the effectiveness and confounding factors of penetrating AK. Diagnoses: The chart of 95 patients with corneal astigmatism (range: 0.75–3.25 diopters [D]) who received penetrating AK from January 2014 to December 2016 was collected. The corneal astigmatism were measured by an autokeratometer (Topcon KR8100PA topographer-autorefractor), and repeated with manual keratometer in low reproducibility cases. Interventions: All patients received penetrating AK by an experienced ophthalmologist (Dr. Gow-Lieng Tseng, MD, PHD) in the operation room. Among which, 66 patients received penetrating AK with phacoemulsification simultaneously (group A), whereas 29 patients received penetrating AK at least 3 months after phacoemulsification (group B). After excluding the patients combined with other procedures or lost followed up, 79 patients are remaining for analysis. The outcome was evaluated by net correction, the difference between preoperative corneal astigmatism (PCA) and residual corneal astigmatism (RCA). Two sample t tests and Pearson test were used for effectiveness evaluation. For confounding factors, multivariate linear regression was used for statistical analysis. Outcomes: The mean preoperative and postoperative refractive cylinders were 1.97 ± 0.77 and 1.08 ± 0.64 D, respectively, in group A and 2.62 ± 1.05 and 1.51 ± 0.89 D in group B. There were no statistically significant differences in net correction between these two groups (0.9 ± 0.66 vs. 1.1 ± 0.69, P = .214). Higher PCA were associated with higher net correction in both group A (P = .002) and group B (P = .019). Compound myopic astigmatism caused less net correction than others only in group A (P = 0.031). Lessons: Penetrating AK is an accessible, affordable, and effective way to correct corneal astigmatism. The results of this procedure are comparable to modern methods in patients with low to moderate corneal astigmatism.
Developmental Trajectories of Executive and Verbal Processes in Children with Phenylketonuria

ABSTRACT Phenylketonuria (PKU) is a hereditary disorder characterized by disrupted phenylalanine metabolism and cognitive impairment. However, the precise nature and developmental trajectory of this cognitive impairment remains unclear. The present study used a verbal fluency task to dissociate executive and verbal processes in children with PKU (n = 23; 7–18 years) and controls (n = 44; 7–19 years). Data were collected at three longitudinal timepoints over a three-year period, and the contributions of age, group, and their interaction to fluency performance were evaluated. Results indicated impairments in executive processes in children with PKU, which were exacerbated by declining metabolic control.
Divided attention enhances explicit but not implicit conceptual memory: an item-specific account of the attentional boost effect

ABSTRACT The Attentional Boost Effect (ABE) refers to the counterintuitive finding that words encoded with to-be-responded targets in a divided-attention condition are remembered better than words encoded with distractors. Previous studies suggested that the ABE-related enhancement of verbal memory depends upon the activation of abstract lexical representations. In the present study, we extend this hypothesis by embedding it in the context of a broader perspective, which proposes that divided attention in the ABE paradigm affects item-specific, but not relational, processing. To this purpose, we examined the ABE in the matched tasks of category-cued recall (CCRT: explicit memory) and category exemplar generation (CEGT: implicit memory). In addition, study time was varied (500, 1500 or 4000 ms), to further determine whether the attentional boost manipulation could influence late-phase elaborative processing. In agreement with the predictions of the item-specific account, the results showed that exemplars encoded with targets were recalled better than exemplars encoded with distractors in the CCRT, but not in the CEGT. Moreover, performance in the CCRT increased with study time, whereas the size of the ABE-related enhancement tended to decrease, further confirming that this effect hinges upon early phase encoding processes.