Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitochondrial genome of the Ptychobarbus kaznakovi (Cyprinidae: Schizothoracinae)

Abstract Ptychobarbus kaznakovi is endemic to the Qinghai-Tibet Plateau in China. The complete mitochondrial genome of P. kaznakovi was sequenced and characterized. The genome is 16 700 bp in length and contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region. The gene arrangement and nucleotide composition of the mitochondrial genome are similar to those of Cyprinidae fish. A 2 bp tandem repeat was identified in the control region. We conclude that the control region is variable in length between and within species. The complete mitochondrial DNA in this study should be used in the studies on population genetics and phylogeny of P. kaznakovi.
Darwin and the Making of Sexual Selection

‘worthy of [his] attention’ (p. 77). Such correspondence could serve as a pedagogical tool for scholars teaching their students the social and linguistic conventions of this era, as these letters provide a conduit through which to explore the role of women in science more broadly during the Victorian period. Indeed, as this collection illuminates, in addition to relying upon their often invisible intellectual labour, men of science depended upon the social finesse of their wives and female allies to advance their careers. Women organized the social functions at which men circulated and often served as diplomatic intermediaries between scientists, carefully and tactfully negotiating sensitive topics and the male ego. Women also managed the scientific reputations of their husbands and, when they became widows, secured their former spouses’ legacies by gathering and promoting their unpublished works. Women additionally played central roles in men’s finances. For example, in 1873, Katherine Murray Lyell, the wife of Charles Lyell, organized a fundraiser for Thomas Henry Huxley, who had fallen on hard times, and in 1879 Arabella Buckley, Alfred Russel Wallace’s secretary, wrote to Darwin asking him to help acquire a government pension for Wallace, who was too ‘modest & sensitive’ to broach the subject himself (p. 63). Darwin and Women challenges the reader to think of the women featured in the collection as more than simply the ‘wife of’ or the ‘daughter of’, and to consider them instead as intelligent and savvy. Accordingly, the editorial commentary at the beginning of each section situates women within the social, economic and political context of Victorian England. For example, the introduction to the section ‘Children’ discusses the high infant and mother mortality rate during this period, and the opening remarks for the section ‘Observing Plants’ examine why botany was a popular and respectable topic of study for women. But while these remarks provide useful context for the letters, Darwin and Women would have been improved by more comprehensive descriptions of the scientific figures and topics discussed and alluded to in the letters. Readers unfamiliar with Lyell, Wallace, Huxley and others may find the brief editorial remarks insufficient. There is a glossary at the end of the book; however, the descriptions provided in it are also rather cursory. Although greater attention to these figures and topics would have extended the length of the book and perhaps diverted attention away from the women featured, it also would have helped this volume to reach a broader audience. Nevertheless, Darwin and Women is a valuable and important collection, and it deserves a place on the bookshelves of those interested in the Victorian period, the development of Darwin’s ideas and women’s contributions to nineteenth-century science.
Indicators and Prevalence of Malnutrition in Motor Neurone Disease

We investigated the nutritional status of a cross-sectional sample of 47 patients with motor neurone disease (MND). Anthropometric measurements (mid-arm circumference and triceps skinfold thickness) and dietary analysis were taken by a trained observer. 21% of patients were moderately to severely malnourished. Patients with bulbar onset were no more likely to be malnourished than patients with limb onset. Measurements of mid-upper-arm muscle circumference indicated that men were more malnourished than women (p = 0.002). We conclude that malnutrition is more prevalent than generally appreciated in patients with MND, including those who do not have swallowing difficulties.
An In–Laboratory Validity and Reliability Tested System for Quantifying Hand–Arm Tremor in Motions

Despite the advancement of the tremor assessment systems, the current technology still lacks a method that can objectively characterize tremors in relative segmental movements. This paper presents a measurement system, which quantifies multi-degrees-of-freedom coupled relative motions of hand–arm tremor, in terms of joint angular displacement. In-laboratory validity and reliability tests of the system algorithm to provide joint angular displacement was carried out by using the two-degrees-of-freedom tremor simulator with incremental rotary encoder systems installed. The statistical analyses show that the developed system has high validity results and comparable reliability performances using the rotary encoder system as the reference. In the clinical trials, the system was tested on 38 Parkinson’s disease patients. The system readings were correlated with the observational tremor ratings of six trained medical doctors. The moderate to very high clinical correlations of the system readings in measuring rest, postural and task-specific tremors add merits to the degree of readiness of the developed tremor measurement system in a routine clinical setting and/or intervention trial for tremor amelioration.
Emerging Applications for Optically Enabled Intravital Microscopic Imaging in Radiobiology

Radiation therapy is an effective cancer treatment used in over 50% of cancer patients. Preclinical research in radiobiology plays a major role in influencing the translation of radiotherapy-based treatment strategies into clinical practice. Studies have demonstrated that various components of tumors and their microenvironments, including vasculature, immune and stem cells, and stromal cells, can influence the response of solid tumors to radiation. Optically enabled imaging techniques used in experimental animal models of cancer offer a unique and powerful way to quantitatively track spatiotemporal changes in these tumor components in vivo at macro-, meso-, and microscopic resolutions following radiotherapy. In this review, we discuss the role of both well-established and emerging intravital microscopy techniques for studying tumors and their microenvironment in vivo, in response to irradiation. The development and application of new animal models, small animal microirradiation technologies, and multimodal optically enabled intravital microscopy techniques are emphasized within the framework of preclinical radiobiology research. We also comment on the potential influence that these newer imaging techniques may have on the clinical translation of new preclinical radiobiology discoveries.
Frequency, Diagnosis, Treatment, and Outcome of Gastrointestinal Disease in Granulomatosis with Polyangiitis and Microscopic Polyangiitis

Objective. Involvement of the gastrointestinal (GI) tract is a rare complication of granulomatosis with polyangiitis (GPA) and microscopic polyangiitis (MPA). The aim was to describe frequency, diagnosis, treatment, and outcome of GI disease in a large series of patients in a single center. Methods. A database that includes all patients with GPA and MPA diagnosed since 1997 in a defined area of southeastern Sweden as well as prevalent older cases and tertiary referral patients was screened for patients with GI disease. Data were retrieved from the patient’s medical records, and GI manifestations of vasculitis were defined as proposed by Pagnoux, et al in 2005. Results. Fourteen (6.5%) of 216 consecutive patients with GPA/MPA had GI manifestations. Abdominal pain and GI bleeding were the most common symptoms. Radiology was important for detection of GI disease, while endoscopy failed to support the diagnosis in many patients. Because of perforation, 5 patients underwent hemicolectomy or small intestine resection. Primary anastomosis was created in 2/5 and enterostomy in 3/5 patients. One patient had a hemicolectomy because of lower GI bleeding. One sigmoid abscess was treated with drainage, and 1 intraabdominal bleeding condition with arterial coiling. Two patients died from GI disease. GPA and MPA patients with and without GI disease exhibited a similar overall survival. Conclusion. GI disease was found in 6.5% among 216 patients with GPA or MPA. Surgery was judged necessary only in cases with GI perforation or severe bleeding. Multidisciplinary engagement is strongly recommended.
Plasma cholesterol concentrations in twin children: estimates of genetic and environmental influences.

Because increased plasma cholesterol is a risk factor for cardiovascular disease, an important question concerns the degree to which this risk is attributable to genetic or environmental influences. Previous studies, largely consisting of older children and adult twin pairs, have indicated environmental contribution to the variation of cholesterol concentration among individuals of 7–68% in the populations evaluated (1)(2)(3)(4)(5). We performed a study to determine the extent of genetic and environmental influences on plasma cholesterol in pairs of twin children ages 2–9 years. We are not aware of similar studies in this age group. A complete age profile addressing the question of environmental vs genetic influence on serum cholesterol is important because the finding of a substantial environmental influence would encourage vigilance for controlling cardiovascular disease risk factors beginning at an early age. The subjects were 57 pairs of healthy twin children between the ages …
Modification of initial therapy in early and advanced Hodgkin lymphoma, based on interim PET/CT is beneficial: a prospective multicentre trial of 355 patients

This multicentre study evaluated 5‐year progression‐free (PFS) and overall survival (OS) in early and advanced Hodgkin lymphoma (HL), where therapy was individualized based on initial prognostic factors and positron emission tomography‐computed tomography performed after two cycles (PET‐2). Between September 2006 and August 2013, 359 patients aged 18–60 years, were recruited in nine Israeli centres. Early‐HL patients initially received ABVD (adriamycin, bleomycin, vinblastine, dacarbazine) ×2. Depending on initial unfavourable prognostic features, PET‐2‐positive patients received additional ABVD followed by involved‐site radiotherapy (ISRT). Patients with negative PET‐2 and favourable disease received ISRT or ABVD ×2; those with unfavourable disease received ABVD ×2 with ISRT or, alternatively, ABVD ×4. Advanced‐HL patients initially received ABVD ×2 or escalated BEACOPP (bleomycin, etoposide, adriamycin, cyclophosphamide, vincristine, procarbazine, prednisone; EB) ×2 based on their international prognostic score (≤2 or ≥3). PET‐2‐negative patients further received ABVD ×4; PET‐2‐positive patients received EB ×4 and ISRT to residual masses. With a median follow‐up of 55 (13–119) months, 5‐year PFS was 91% and 69% for PET‐2‐negative and positive early‐HL, respectively; 5‐year OS was 100% and 95%, respectively. For advanced‐HL, the PFS was 81% and 68%, respectively (P = 0·08); 5‐year OS was 98% and 91%, respectively. PET‐2 positivity is associated with inferior prognosis in early‐HL, even with additional ABVD and ISRT. Advanced‐HL patients benefit from therapy escalation following positive PET‐2. EB can be safely de‐escalated to ABVD in PET‐2‐negative patients.
Efficacy and Safety of Individualized Coaching After Stroke: the LAST Study (Life After Stroke) A Pragmatic Randomized Controlled Trial

Background and Purpose— The evidence for interventions to prevent functional decline in the long term after stroke is lacking. The aim of this trial was to evaluate the efficacy and safety of an 18-month follow-up program of individualized regular coaching on physical activity and exercise. Methods— This was a multicentre, pragmatic, single-blinded, randomized controlled trial. Adults (age ≥18 years) with first-ever or recurrent stroke, community dwelling, with modified Rankin Scale <5, and no serious comorbidities were included 10 to 16 weeks poststroke. The intervention group received individualized regular coaching on physical activity and exercise every month for 18 consecutive months. The control group received standard care. Primary outcome was the Motor Assessment Scale at end of intervention (18-month follow-up). Secondary measures were Barthel index, modified Rankin Scale, item 14 from Berg Balance Scale, Timed Up and Go test, gait speed, 6-minute walk test, and Stroke Impact Scale. Other outcomes were adverse events and compliance to the intervention assessed by training diaries and the International Physical Activity Questionnaire. Results— Three hundred and eighty consenting participants were randomly assigned to individualized coaching (n=186) or standard care (n=194). The mean estimated difference on Motor Assessment Scale in favor of control group was −0.70 points (95% confidence interval, −2.80, 1.39), P=0.512. There were no differences between the groups on Barthel index, modified Rankin Scale, or Berg Balance Scale. The frequency of adverse events was low in both groups. Results from International Physical Activity Questionnaire and training diaries showed increased activity levels but low intensity of the exercise in the intervention group. Conclusions— The regular individualized coaching did not improve maintenance of motor function or the secondary outcomes compared with standard care. The intervention should be regarded as safe. Despite the neutral results, the health costs related to the intervention should be investigated. Clinical Trial Registration— URL: https://www.clinicaltrials. gov. Unique identifier: NCT01467206.
Exploratory reconstructability analysis of accident TBI data

Abstract This paper describes the use of reconstructability analysis to perform a secondary study of traumatic brain injury data from automobile accidents. Neutral searches were done and their results displayed with a hypergraph. Directed searches, using both variable-based and state-based models, were applied to predict performance on two cognitive tests and one neurological test. Very simple state-based models gave large uncertainty reductions for all three DVs and sizeable improvements in percent correct for the two cognitive test DVs which were equally sampled. Conditional probability distributions for these models are easily visualized with simple decision trees. Confounding variables and counter-intuitive findings are also reported.
Cattle gene mapping by somatic cell hybridization study of 17 enzyme markers.

In 38 independent hamster-bovine hybrids, the segregation of 17 bovine enzyme markers was studied. The results showed three syntenic groups; LDHB-PEPB-TPI, PGM3-ME1-SOD2, and PGD-ENOl, whereas nine other markers did not show any syntenic relationship: LDHA, MDH2, LDH1, SOD1, PKM2, PGM1, PGM2, AK1, and MPI.
An Improved Multi-Output Gaussian Process RNN with Real-Time Validation for Early Sepsis Detection

Sepsis is a poorly understood and potentially life-threatening complication that can occur as a result of infection. Early detection and treatment improves patient outcomes, and as such it poses an important challenge in medicine. In this work, we develop a flexible classifier that leverages streaming lab results, vitals, and medications to predict sepsis before it occurs. We model patient clinical time series with multi-output Gaussian processes, maintaining uncertainty about the physiological state of a patient while also imputing missing values. The mean function takes into account the effects of medications administered on the trajectories of the physiological variables. Latent function values from the Gaussian process are then fed into a deep recurrent neural network to classify patient encounters as septic or not, and the overall model is trained end-to-end using back-propagation. We train and validate our model on a large dataset of 18 months of heterogeneous inpatient stays from the Duke University Health System, and develop a new "real-time" validation scheme for simulating the performance of our model as it will actually be used. Our proposed method substantially outperforms clinical baselines, and improves on a previous related model for detecting sepsis. Our model's predictions will be displayed in a real-time analytics dashboard to be used by a sepsis rapid response team to help detect and improve treatment of sepsis.
Identification of Estrogen-Related Receptor &agr; Agonists in the Tox21 Compound Library

The estrogen-related receptor α (ERRα) is an orphan nuclear receptor (NR) that plays a role in energy homeostasis and controls mitochondrial oxidative respiration. Increased expression of ERRα in certain ovarian, breast, and colon cancers has a negative prognosis, indicating an important role for ERRα in cancer progression. An interaction between ERRα and peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) has also recently been shown to regulate an enzyme in the β-oxidation of free fatty acids, thereby suggesting that ERRα plays an important role in obesity and type 2 diabetes. Therefore, it would be prudent to identify compounds that can act as activators of ERRα. In this study, we screened ∼10,000 (8311 unique) compounds, known as the Tox21 10K collection, to identify agonists of ERRα. We performed this screen using two stably transfected HEK 293 cell lines, one with the ERRα-reporter alone and the other with both ERRα-reporter and PGC-1α expression vectors. After the primary screening, we identified more than five agonist clusters based on compound structural similarity analysis (e.g., statins). By examining the activities of the confirmed ERRα modulators in other Tox21 NR assays, eliminating those with promiscuous NR activity, and performing follow-up assays (e.g., small interfering RNA knockdown), we identified compounds that might act as endocrine disrupters through effects on ERRα signaling. To our knowledge, this study is the first comprehensive analysis in discovering potential endocrine disrupters that affect the ERRα signaling pathway.
Markov regime switching in mean and in fractional integration parameter

ABSTRACT We propose a specific general Markov-regime switching estimation both in the long memory parameter d and the mean of a time series. We employ Viterbi algorithm that combines the Viterbi procedures in two state Markov-switching parameter estimation. It is well-known that existence of mean break and long memory in time series can be easily confused with each other in most cases. Thus, we aim at observing the deviation and interaction of mean and d estimates for different cases. A Monte Carlo experiment reveals that the finite sample performance of the proposed algorithm for a simple mixture model of Markov-switching mean and d changes with respect to the fractional integrating parameters and the mean values for the two regimes.
Design of a pyroelectric charge amplifier and a piezoelectric energy harvester for a novel non-invasive wearable and self-powered respiratory monitoring system

The paper presents a novel method of respiratory monitoring system based on pyroelectric material-based sensors. The system is designed to be convenient for the neonatal infants having a chronic breathing disorder known as apnea of prematurity. The front-end circuitry is designed in a 130 nm standard CMOS process. The incorporated design topology enables the system to operate with a lower cut-off frequency below 10 mHz with a noise efficiency factor as low as 2.79. The respiration monitoring system consists of a non-invasive wearable device that consumes very low power and has the potential to be self-powered by harvesting energy from a piezoelectric transducer. The overall system is very light-weight and requires attaching fewer electrodes and wires to the patient's body in comparison with the standard methods of respiration monitoring for apnea patients.
A Staufen1-mediated decay pathway influences the local transcriptome in axons

ABSTRACT Local translation is critical for diverse aspects of neuronal function, including mediating responses of elongating axons to guidance cues and other signaling molecules. A major determinant of the protein synthetic capacity of axons and growth cones is the specific set of mRNAs that are trafficked to these sites. However, recently it has become clear that the axonal transcriptome can also be shaped by local RNA degradation mechanisms, such as nonsense-mediated decay. Here we show that Staufen1-mediated decay can also occur within axons and mediate degradation of specific axonal transcripts. We show that Staufen1 and Upf1, which function together in Staufen1-mediated decay, are localized in growth cones. Selective depletion of Staufen1 from neurons results in a complex pattern of transcriptional alterations, with a subset of transcripts showing increased expression and increased RNA half-life consistent with their regulation by Staufen1-mediated decay. Additionally, we show certain transcripts, such as Rac1, are regulated by Staufen1 within axons and growth cones. The functional significance of Staufen1 in growth cones is supported by morphological alterations in growth cones following Staufen1 knockdown. Together these data point to Staufen1-mediated decay as a novel mechanism to control mRNA expression levels in axons and growth cones through local RNA degradation.
FPGA-based stepper motor vector control system design

In this paper, we implement a stepper motor drive system on field programmable gate array (FPGA), and the design is mainly based on vector control strategy. First, the control system is built by MATLAB/Simulink and simulated on Modelsim platform. Next, the resulting software system is converted into Verilog HDL codes, and implemented on an Altera Cyclone III FPGA. The stator's currents of the developed hardware system are first shown by simulation and experiment to verify the validness and performances of the vector control structure. After that, the speed responses of motor rotor are shown to prove the performances of the outer loop control system and encoder counter circuit.