Miracle-dz/UniFAR-FTUs huggingface dataset:
Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail millet. Recently, the 510 Mb genome of foxtail millet, S. italica, has been sequenced 1,2 and a 25x coverage genome sequence of the weedy relative S. viridis is in progress. S. viridis has a number of characteristics that make it a potentially excellent model genetic system including a rapid generation time, small stature, simple growth requirements, prolific seed production 3 and developed systems for both transient and stable transformation 4. However, the genetics of S. viridis is largely unexplored, in part, due to the lack of detailed methods for performing crosses. To date, no standard protocol has been adopted that will permit rapid production of seeds from controlled crosses. The protocol presented here is optimized for performing genetic crosses in S. viridis, accession A10.1. We have employed a simple heat treatment with warm water for emasculation after pruning the panicle to retain 20-30 florets and labeling of flowers to eliminate seeds resulting from newly developed flowers after emasculation. After testing a series of heat treatments at permissive temperatures and varying the duration of dipping, we have established an optimum temperature and time range of 48 °C for 3-6 min. By using this method, a minimum of 15 crosses can be performed by a single worker per day and an average of 3-5 outcross progeny per panicle can be recovered. Therefore, an average of 45-75 outcross progeny can be produced by one person in a single day. Broad implementation of this technique will facilitate the development of recombinant inbred line populations of S. viridis X S. viridis or S. viridis X S. italica, mapping mutations through bulk segregant analysis and creating higher order mutants for genetic analysis.
Psychoactive drug use by young and future physicians.

Drug-use surveys of nonclinical samples of young physicians and premedical, medical, and nursing students in New England indicate that between 56 and 70 percent have used marijuana and that some of them now have progressed to recreational experimentation with higher-risk drugs, especially cocaine (15 to 21 percent). At the same time, use of amphetamines for studying and staying awake appears to have declined in prevalence. These figures reflect the influence of current drug-use trends among university populations, although future health professionals consistently have slightly lower drug-use rates than many other graduate and college students. Approximately 40 percent of the young physicians also treated themselves with one or more psychoactive drugs, mostly opiates (27 percent), tranquilizers (17 percent), and sedatives (8 percent). Although most subjects have used drugs only afew times, some reported more regular use; the latter therefore may be at risk of developing drug problems.
Renal sodium handling in acute and chronic salt loading/depletion protocols: the confounding influence of acute water loading

Objectives Renal tubular sodium handling was measured in healthy subjects submitted to acute and chronic salt-repletion/salt-depletion protocols. The goal was to compare the changes in proximal and distal sodium handling induced by the two procedures using the lithium clearance technique. Methods In nine subjects, acute salt loading was obtained with a 2 h infusion of isotonic saline, and salt depletion was induced with a low-salt diet and furosemide. In the chronic protocol, 15 subjects randomly received a low-, a regular-and a high-sodium diet for 1 week. In both protocols, renal and systemic haemodynamics and urinary electrolyte excretion were measured after an acute water load. In the chronic study, sodium handling was also determined, based on 12 h day-and night-time urine collections. Results The acute and chronic protocols induced comparable changes in sodium excretion, renal haemodynamics and hormonal responses. Yet, the relative contribution of the proximal and distal nephrons to sodium excretion in response to salt loading and depletion differed in the two protocols. Acutely, subjects appeared to regulate sodium balance mainly by the distal nephron, with little contribution of the proximal tubule. In contrast, in the chronic protocol, changes in sodium reabsorption could be measured both in the proximal and distal nephrons. Acute water loading was an important confounding factor which increased sodium excretion by reducing proximal sodium reabsorption. This interference of water was particularly marked in salt-depleted subjects. Conclusion Acute and chronic salt loading/salt depletion protocols investigate different renal mechanisms of control of sodium balance. The endogenous lithium clearance technique is a reliable method to assess proximal sodium reabsorption in humans. However, to investigate sodium handling in diseases such as hypertension, lithium should be measured preferably on 24 h or overnight urine collections to avoid the confounding influence of water.
Biomechanical study of distal radioulnar joint ballottement test

We investigated the reliability and accuracy of the distal radioulnar joint (DRUJ) ballottement test using five fresh‐frozen cadaver specimens in triangular fibrocartilage complex (TFCC)‐intact, and TFCC‐sectioned wrists. The humerus and proximal ulna were fixed. The ulna was allowed to translate in dorsopalmar directions without rotation, and the radius was allowed to move freely. Four sensors of a magnetic tracking system were attached to the radius and ulna, and the nails of each examiner's thumbs. Five examiners conducted the DRUJ ballottement test before and after TFCC sectioning. We used two techniques: With holding and without holding the carpal bones to the radius (holding and non‐holding tests, respectively). We compared the magnitudes of bone‐to‐bone (absolute DRUJ) movement with that of the examiner's nail‐to‐nail (relative DRUJ) movement. The intrarater intraclass correlation coefficients (ICCs) were 0.92 (holding) and 0.94 (non‐holding). The interrater ICCs were 0.84 (holding) and 0.75 (non‐holding). Magnitudes of absolute and relative movements averaged 11.5 and 11.8 mm, respectively (p < 0.05). Before TFCC sectioning, the DRUJ movement during the holding and non‐holding techniques averaged 9.8 and 10.8 mm, respectively (p < 0.05). The increase in DRUJ movement after TFCC sectioning was greater with the holding technique (average 2.3 mm) than with the non‐holding technique (average 1.6 mm). The DRUJ ballottement test with magnetic markers is relatively accurate and reliable for detecting unstable joints. We recommend the holding technique for assessing DRUJ instability in clinical practice. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1123–1127, 2017.
L-Cysteine Improves Growth of Human Peritoneal Mesothelial Cells In Vitro

Objective To improve the growth characteristics of human peritoneal mesothelial cells (HPMC). Design The effect of commonly used agents, L-cysteine and epidermal growth factor (EGF), added individually (“single”) or mixed with hydrocortisone and apo-transferrin (“admixture”) in the culture medium (M199) on cultured HPMC, was investigated. Methods: Growth agents were added to M199 medium along with 2% fetal bovine serum and L-glutamine. Growth was determined by the analysis of thymidine ([methyl-3H] thymidine) incorporation into deoxyribonucleic acid, total cell protein, and by cell counts. Morphology was assessed by phase contrast light microscopy and scanning electron microscopy. Results HPMC exposed to L-cysteine 0.25 x 10–3 mol/L (30 μg/mL) exhibited significantly improved attachment and growth. Attached cells appeared flat and well spread out shortly after seeding, and produced a tight polygonal monolayer in 14 days, in contrast to the growth of HPMC in control M199 medium, which failed to reach confluence. After an initial lag period in cell growth, EGF (0.01 μg/mL) produced a greater increase in cell growth than L-cysteine did; however, this was associated with changes in HPMC morphology. During the growth period (14 days), EGF-stimulated HPMC appeared distorted and irregular compared to L-cysteine-treated cells, which had the characteristic tight “cobblestone” appearance. Conclusion L-cysteine improved cell attachment with preservation of the characteristic morphology of HPMC. Epidermal growth factor improved cell growth but produced changes in morphology. The addition of L-cysteine to the culture medium has an important cell growth enhancement role due to the improved cell attachment and cell viability.
A simple process algebra based on atomic actions with resources

This paper initiates the study of a process algebra based on atomic actions that are assigned resources, and that supports true concurrency. By true concurrency we mean that the parallel composition of concurrent processes does not rely on an interleaving of concurrent actions for its definition. Our process algebra includes a number of interesting operators that can be defined using resources of atomic actions to control their behaviour: of particular note is a (weak) sequential composition operator that exploits the truly concurrent nature of the semantics; this operator extends significantly the operation of prefixing by atomic actions that is supported in most truly concurrent semantics. Our language also includes a parallel composition operator that allows local events to execute asynchronously, while requiring synchronising events to execute simultaneously. In addition, the language supports a restriction operator and includes (unguarded) recursion. We present both a denotational semantics and a companion operational semantics for our language. The denotational semantics supports true concurrency, so that parallel composition is defined without non-determinism or interleaving. This semantics also is novel for its treatment of recursion. The meaning of a recursive process is defined using a least fixed point on a subdomain that is determined by the body of the recursion, and that varies from one process to another. Nonetheless, the recursion operators in the language have continuous interpretations in the denotational model. In fact, our denotational model is based on a domain-theoretic generalisation of Mazurkiewicz traces in which the concatenation operator, as well as the other operators from our language, can be given continuous interpretations. The operational model is presented in a natural SOS style. We prove a congruence theorem relating the two semantics, which implies the operational model itself is compositional. The congruence theorem also implies the denotational model is adequate with respect to the operational semantics, and we characterise the relatively mild conditions under which the denotational semantics is fully abstract with respect to the operational semantics.
A classification of unanticipated runtime software changes in Java

For some software systems with high availability requirements, it is not acceptable to have the system shut down when a new version of it is to be deployed. An alternative is to use unanticipated runtime software evolution, which means making changes to the software system while it is executing. We propose a classification of unanticipated runtime software changes. Our classification consists of a code change aspect, a state change aspect and an activity aspect. The purpose of the classification is to get a greater understanding of the nature of such changes, and to facilitate an abstract view of them. We also present results from a case study, where historical changes to an existing software system have been categorized according to the classification. The data from the case study gives an indication that the Java Platform Debugger Architecture, a standard mechanism in Java virtual machines, is a viable technical foundation for runtime software evolution systems.
Short Term Insulin Treatment Prevents the Diabetogenic Action of Streptozotocin in Rats1.

Streptozotocin, which induces diabetes mellitus in experimental animals, has been reported to be taken up by β-cells by means of the glucose transporter 2 (GLUT2) and then reduce the cellular level of NAD+, leading to necrosis of the β-cells. We investigated the effect of insulin pretreatment on the diabetogenic action of streptozotocin (60 mg/kg). Four groups of rats were studied: 1) a group that received streptozotocin (STZ), 2) a group that received insulin pretreatment and streptozotocin (INS+STZ), 3) a group that received insulin (INS), and 4) a control group (CTRL). Insulin treatment reduced the β-cell immunoreactivity (IR) of insulin and GLUT2, which, thus, was reduced in INS+STZ rats at the time of streptozotocin injection. In STZ rats, plasma insulin concentrations after 3 weeks as well as insulin concentrations in pancreatic tissue samples were significantly lower than those in CTRL rats [plasma, 274.3 ± 101.9 vs. 1078.8 ± 254.9 pmol/liter (P < 0.05); tissue, 0.46 ± 0.02 vs. 117.0 ± 28.4 nmol/g .
What do our patients understand about their trial participation? Assessing patients' understanding of their informed consent consultation about randomised clinical trials

Background Ethically, informed consent regarding randomised controlled trials (RCTs) should be understandable to patients. The patients can then give free consent or decline to participate in a RCT. Little is known about what patients really understand in consultations about RCTs. Methods Cancer patients who were asked to participate in a randomised trial were surveyed using a semi-standardised interview developed by the authors. The interview addresses understanding, satisfaction and needs of the patients. The sample included eight patients who participated in a trial and two who declined. The data were analysed on the basis of Mayring's qualitative analysis. Results Patients' understanding of informed consent was less developed than anticipated, especially concerning key elements such as randomisation, content and procedure of RCTs. Analysing the result about satisfaction of the patients, most of the patients described their consultations as hectic and without advance notice. Health limitations due to cancer played a decisive role. However, most of the patients perceived their physician to be sympathetic. Analysing the needs of patients, they ask for a clear informed consent consultation with enough time and adequate advance notice. Conclusion This study fills an important empirical research gap of what is ethically demanded in an RCT consultation and what is really understood by patients. The qualitative approach enabled us to obtain new results about cancer patients' understanding of informed consent, to clarify patients' needs and to develop new ideas to optimise the informed consent.
Pharmacotherapy in Parkinson’s disease: case studies

Parkinson’s disease is a common neurodegenerative disorder with the particular feature of having various available treatments with proven efficacy. However, no treatment is curative. Recent trial results provided data for the discussion about the potential disease-modifying effect of new drugs as well as of other therapeutic strategies. The changing clinical phenotype following the progression of the disease multiplies the number of treatment targets and makes the application of recommendations from guidelines or other treatment algorithms to the individual patient a complex task. In the present manuscript, we discuss the treatment management of three case studies illustrating different stages of disease with distinct phenomenology. The proposed therapeutic alternatives are discussed based on the best data available; that is, treatment guidelines, clinical trial results or observational data.
An Expedited Forwarding PHB

The definition of PHBs (per-hop forwarding behaviors) is a critical part of the work of the Diffserv Working Group. This document describes a PHB called Expedited Forwarding. We show the generality of this PHB by noting that it can be produced by more than one mechanism and give an example of its use to produce at least one service, a Virtual Leased Line. A recommended codepoint for this PHB is given.
Flexibility in children with autism spectrum disorders (ASD): Inconsistency between neuropsychological tests and parent-based rating scales

In this study, we compared neuropsychological tests and parent-based ratings of flexibility in a sample of children with autism spectrum disorders (ASD). We investigated the discriminant validity of the domain-specific flexibility measures by comparison with the domain general measures, general behavioral problems, general ASD-related traits, and general intelligence. Tests and parent-based ratings of flexibility were not significantly correlated. Parent-based ratings were strongly related with the three broadband measures, whereas the discriminant validity indices of the neuropsychological tests were satisfactory. These findings suggest that parent-based ratings do not reflect the specific executive construct of flexibility, but instead reflect a broad spectrum of general child characteristics.
Tibiofemoral contact mechanics following a horizontal cleavage lesion in the posterior horn of the medial meniscus

The purpose of this study was to determine if a horizontal cleavage lesion (HCL) of the posterior horn of the medial meniscus would result in changes to tibiofemoral contact mechanics, as measured by peak contact pressure and contact area, which can lead to cartilage degeneration. To study this, 10 cadaveric knees were tested in a rig where forces were applied (500 N Compression, 100 N shear, 2.5 Nm Torque) and the knee dynamically flexed from −5° to 135°, as peak contact pressure and contact area were recorded. After testing of the intact knee, a horizontal cleavage lesion was created arthroscopically and testing repeated. The Wilcoxon signed‐rank test was used to determine if there were differences in peak contact pressure and contact area between the intact knee and that with the HCL. A statistically significant increase in peak contact pressure of 13%, on average, and a decrease in contact area of 6%, on average, was noted following the HCL. This suggests that a horizontal cleavage lesion will result in small but statistically significant changes in tibiofemoral contact mechanics which may lead to cartilage degeneration. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:584–590, 2015.
Robotic catheter cardiac ablation combining ultrasound guidance and force control

Cardiac catheters allow physicians to access the inside of the heart and perform therapeutic interventions without stopping the heart or opening the chest. However, conventional manual and actuated cardiac catheters are currently unable to precisely track and manipulate the intracardiac tissue structures because of the fast tissue motion and potential for applying damaging forces. This paper addresses these challenges by proposing and implementing a robotic catheter system that uses 3D ultrasound image guidance and force control to enable constant contact with a moving target surface in order to perform interventional procedures, such as intracardiac tissue ablation. The robotic catheter system, consisting of a catheter module, ablation and force sensing end effector, drive system, and image-guidance and control system, was commanded to apply a constant force against a moving target using a position-modulated force control method. The control system uses a combination of position tracking, force feedback, and friction and backlash compensation to achieve accurate and safe catheter–tissue interactions. The catheter was able to maintain a 1 N force on a moving motion simulator target under ultrasound guidance with 0.08 N RMS error. In a simulated ablation experiment, the robotic catheter was also able to apply a consistent force on the target while maintaining ablation electrode contact with 97% less RMS contact resistance variation than a passive mechanical equivalent. In addition, the use of force control improved catheter motion tracking by approximately 20%. These results demonstrate that 3D ultrasound guidance and force tracking allow the robotic system to maintain improved contact with a moving tissue structure, thus allowing for more accurate and repeatable cardiac procedures.
Cidofovir bladder instillation for the treatment of BK hemorrhagic cystitis after allogeneic stem cell transplantation

We report a case of severe hemorrhagic cystitis after allogeneic transplantation in association with high BK viral load. After failure of aggressive hydration, platelet and blood transfusions, continuous bladder irrigation, and tapering of the immune suppression, we instilled cidofovir into the bladder, which resulted in decreased BK viral load and significant clinical improvement. Our case suggests that local cidofovir therapy for viral hemorrhagic cystitis is effective and well tolerated with no observed side effects. Am. J. Hematol. 81:535–537, 2006. © 2006 Wiley‐Liss, Inc.
Precision of Digital Volume Correlation Approaches for Strain Analysis in Bone Imaged with Micro-Computed Tomography at Different Dimensional Levels

Accurate measurement of local strain in heterogeneous and anisotropic bone tissue is fundamental to understand the pathophysiology of musculoskeletal diseases, to evaluate the effect of interventions from preclinical studies, and to optimize the design and delivery of biomaterials. Digital volume correlation (DVC) can be used to measure the three-dimensional displacement and strain fields from micro-Computed Tomography (µCT) images of loaded specimens. However, this approach is affected by the quality of the input images, by the morphology and density of the tissue under investigation, by the correlation scheme, and by the operational parameters used in the computation. Therefore, for each application the precision of the method should be evaluated. In this paper we present the results collected from datasets analyzed in previous studies as well as new data from a recent experimental campaign for characterizing the relationship between the precision of two different DVC approaches and the spatial resolution of the outputs. Different bone structures scanned with laboratory source µCT or Synchrotron light µCT (SRµCT) were processed in zero-strain tests to evaluate the precision of the DVC methods as a function of the subvolume size that ranged from 8 to 2500 micrometers. The results confirmed that for every microstructure the precision of DVC improves for larger subvolume size, following power laws. However, for the first time large differences in the precision of both local and global DVC approaches have been highlighted when SRµCT or in vivo µCT images were used instead of conventional ex vivo µCT. These findings suggest that in situ mechanical testing protocols applied in SRµCT facilities should be optimized in order to allow DVC analyses of localized strain measurements. Moreover, for in vivo µCT applications DVC analyses should be performed only with relatively course spatial resolution for achieving a reasonable precision of the method. In conclusion, we have extensively shown that the precision of both tested DVC approaches is affected by different bone structures, different input image resolution and different subvolume sizes. Before each specific application DVC users should always apply a similar approach to find the best compromise between precision and spatial resolution of the measurements.