Joint Maximum Likelihood of Phylogeny and Ancestral States Is Not Consistent.

Maximum likelihood estimation in phylogenetics requires a means of handling unknown ancestral states. Classical maximum likelihood averages over these unknown intermediate states, leading to provably consistent estimation of the topology and continuous model parameters. Recently, a computationally efficient approach has been proposed to jointly maximize over these unknown states and phylogenetic parameters. Although this method of joint maximum likelihood estimation can obtain estimates more quickly, its properties as an estimator are not yet clear. In this article, we show that this method of jointly estimating phylogenetic parameters along with ancestral states is not consistent in general. We find a sizeable region of parameter space that generates data on a four-taxon tree for which this joint method estimates the internal branch length to be exactly zero, even in the limit of infinite-length sequences. More generally, we show that this joint method only estimates branch lengths correctly on a set of measure zero. We show empirically that branch length estimates are systematically biased downward, even for short branches.

Angiotensin converting enzymes ACE and ACE2 in thyroid cancer progression.

Angiotensin-converting enzymes, ACE and ACE2, play not only a pivotal role in the regulation of blood pressure, but are involved in the processes of pathophysiology, including thyroid dysfunction or progression of several neoplasia such as cancers of skin, lungs, pancreas and leukemia. However, their role in the thyroid carcinogenesis remains unknown. We examined in this study the expression of ACE and ACE2 in thyroid tissues and their possible employment as biomarkers for thyroid cancer progression. Thyroid tissues, including 14 goiters (G), 12 follicular adenomas (FA), 10 follicular thyroid carcinomas (FTC), 14 papillary thyroid carcinomas (PTC) and 11 undifferentiated thyroid carcinomas (UTC), were subjected to RT-PCR and protein analyses with primers or antibodies specific for ACE and ACE2, respectively. FA revealed significantly increased ACE compared to other groups and FTC was significantly higher than UTC. ACE2 was significantly increased in PTC in comparison to G, FA and UTC, and in FTC as compared to G. The ratio ACE/ACE2 decreased, while ACE2/ACE increased with the differentiation grade of thyroid carcinoma. ACE was significantly diminished in individuals older than 50. Both ACEs were significantly diminished in M1 patients, ACE2 additionally in higher tumor masses. ACE and ACE2 are regulated within thyroid benign and malignant tissues. As the transcript ratio between both enzymes correlate proportional with the differentiation status of thyroid cancer, ACE and ACE2 may serve as new markers for thyroid carcinoma.

Differential protein phosphorylation is responsible for hypoxia-induced regulation of the Akt/mTOR pathway in naked mole rats.

Naked mole rats (NMRs, Heterocephalus glaber) are among the most hypoxia-tolerant mammals known. They can reduce their metabolic rate (>85%) under severe hypoxia, remain moderately active and recover with no obvious signs of damage. Hence, NMRs are an excellent model for studying mammalian hypoxia tolerance. The current study characterized the involvement of posttranslational modifications in regulating the Akt/mTOR pathway that regulates protein synthesis, and the responses of key ribosomal proteins in order to assess tissue-specific responses to 4 h exposure to 7% O2 (compared to controls at 21% O2). Results showed a tissue-specific regulation of the Akt/mTOR pathway via differential phosphorylation. Relative amounts of p-TSC(S939) in brain and of p-TSC(S939), p-Akt(473) and p-PTEN(S380) in liver increased under hypoxia, whereas levels of IGF1R(Y1135/1136) in liver decreased. In skeletal muscle, levels of p-Akt(S473) and p-PTEN(S380) decreased during hypoxia, whereas lungs showed an increase in p-mTOR(S2884) content but a decrease in p-RPS6(S235-236) under the same conditions. Analysis of the phosphorylation states of ribosomal proteins revealed increases in p-4E-BP1(T37/46) content in brain and lungs under hypoxia, as well as a rise in total 4E-BP1 protein level in liver. Phosphorylated eIF-4B(S422) content also increased in liver while levels of p-eIF-2α(S51), and eIF-4E(S209) decreased during hypoxia in liver. Overall, hypoxia altered the Akt/mTOR pathway, which correlated with a general decrease in activity of the ribosomal protein biosynthesis machinery in muscle, lung, and brain of NMRs. However, the increase in eIF-4B in liver suggests the potential promotion of cap-independent mRNA translation mechanism operating under hypoxic stress.

Expression of ARE-binding proteins AUF1 and HuR in follicular adenoma and carcinoma of thyroid gland.

Both adenylate-uridylate rich elements binding proteins AUF1 and HuR may participate in thyroid carcinoma progression. In this study we investigated the expression of both factors on a protein level with a special focus on follicular adenoma and follicular thyroid carcinoma. By employment of immunofluorescence and western blot on 68 thyroid tissues including 7 goiter, 16 follicular adenoma (4 adenomatous hyperplasia), 19 follicular thyroid carcinomas, 13 papillary thyroid carcinomas and 14 undifferentiated thyroid carcinomas we investigated protein expression of AUF1 and HuR. In addition to previous results we demonstrated that AUF1 and HuR are significantly up-regulated in carcinoma tissues as compared with follicular adenoma or goiter tissues. Furthermore, by evaluation of AUF1 or HuR expression, or combination of both proteins on total tissue lysates, we were able to demonstrate a significant difference between follicular adenoma and follicular thyroid carcinoma. Overexpression of AUF1 and HuR is a common finding observed in thyroid malignancy. Analysis of the tissues obtained by surgical resection as demonstrated in this study is comparable to a fine needle aspiration and in combination with AUF1/HuR immuno-analysis may support the conventional immunohistological investigations. The promising results of this study were performed on relatively small collective, but justify future development of a quick thyroid diagnostic test on larger cohort of the patients, especially for thyroid samples which are inadequate for histological examinations.

Graft arterial stenosis in kidney en bloc grafts from very small pediatric donors: incidence, timing, and role of ultrasound in screening.

In previous studies with different donor selection criteria and noncontemporary surgical techniques, graft arterial stenosis (GAS) has been reported to occur more frequently in adult recipients of pediatric en bloc renal allografts (EBKT) as compared to single adult donor allografts. The purpose of our study was to evaluate the incidence of GAS within our EBKT recipient population and to evaluate clinical and imaging features of those cases with GAS. In a retrospective cohort study, we analyzed 182 EBKT performed at a single institution. We identified cases of suspected GAS based on clinical factors, lab results, and noninvasive imaging. Diagnosis of GAS was confirmed by digital subtraction angiography. Two EBKT recipients (1.1% of 182) had angiographically confirmed GAS at 2.5 and 4.5 months after transplant. In both cases, the stenoses were short segment within the proximal (perianastomotic) donor aorta, color Doppler ultrasound demonstrated peak systolic velocities of >400 cm/s, and poststenotic parvus tardus waveforms were present. Both patients underwent angioplasty and demonstrated postintervention improvement in renal function and blood pressure. Restenosis did not occur during follow up. In conclusion, recipients of EBKT have a low incidence of GAS, similar to the lowest reported for adult single allografts.

Performance of the Tachyon Time-of-Flight PET Camera.

We have constructed and characterized a time-of-flight Positron Emission Tomography (TOF PET) camera called the Tachyon. The Tachyon is a single-ring Lutetium Oxyorthosilicate (LSO) based camera designed to obtain significantly better timing resolution than the ~ 550 ps found in present commercial TOF cameras, in order to quantify the benefit of improved TOF resolution for clinically relevant tasks. The Tachyon's detector module is optimized for timing by coupling the 6.15 × 25 mm2 side of 6.15 × 6.15 × 25 mm3 LSO scintillator crystals onto a 1-inch diameter Hamamatsu R-9800 PMT with a super-bialkali photocathode. We characterized the camera according to the NEMA NU 2-2012 standard, measuring the energy resolution, timing resolution, spatial resolution, noise equivalent count rates and sensitivity. The Tachyon achieved a coincidence timing resolution of 314 ps +/- ps FWHM over all crystal-crystal combinations. Experiments were performed with the NEMA body phantom to assess the imaging performance improvement over non-TOF PET. The results show that at a matched contrast, incorporating 314 ps TOF reduces the standard deviation of the contrast by a factor of about 2.3.

Factors Affecting Process Temperature and Biogas Production in Small-scale Rural Biogas Digesters in Winter in Northern Vietnam.

This study investigated the main factors influencing digester temperature and methods to reduce heat losses during the cold season in the subtropics. Four composite digesters (two insulated and two uninsulated) were buried underground to measure their internal temperature (°C) at a depth of 140 cm and 180 cm, biogas production and methane (CH4) concentration in biogas from August to February. In parallel the temperature of the air (100 cm above ground), in the slurry mixing tank and in the soil (10, 100, 140, and 180 cm depth) was measured by thermocouple. The influent amount was measured daily and the influent chemical composition was measured monthly during the whole experimental period. Seasonal variations in air temperature significantly affected the temperature in the soil, mixing tank and digester. Consequently, biogas production, which is temperature dependent, was influenced by the season. The main factors determining the internal temperature in the digesters were insulation with Styrofoam, air temperature and temperature of slurry in the mixing tank. Biogas production is low due to the cold climate conditions in winter in Northern Vietnam, but the study proved that storing slurry in the mixing tank until its temperature peak at around 14:00 h will increase the temperature in the digester and thus increase potential biogas production. Algorithms are provided linking digester temperature to the temperature of slurry in the mixing tank.

Pancreatic cystic lesions and guidelines: a review.

No abstract available.

Endoscopic Retrograde Cholangiopancreatography Under General Anesthesia Compared to Conscious Sedation Study.

Background: Endoscopic retrograde cholangiopancreatography (ERCP) is used to diagnose and treat pancreatic and biliary disease. The current standard is to conduct ERCP under conscious sedation (CS). Patient movement and agitation during ERCP under CS can result in procedure failure and complications. Aiming to reduce procedure failure rates and complications, Kelowna General Hospital (KGH) in British Columbia, Canada transitioned to performing ERCP under general anesthesia (GA) as the practice standard. Objective: To determine if conducting ERCP under GA compared to CS decreases procedure complications, particularly post-ERCP pancreatitis (PEP). Methods: The charts of 2,198 patients who underwent ERCP at KGH between 2015 and 2020 were reviewed. Before September 17, 2017, ERCP was performed under CS (n = 1,316). Afterwards, ERCP was conducted under GA (n = 882). Demographic, clinical, and procedural data were extracted. The data were analyzed using univariate and multivariate statistical analysis. Results: Procedure failure rates (CS = 9 percent, GA = 3 percent, P < 0.001) decreased in the GA cohort after adjusting for age, sex, and co-morbidities. Thirty-day mortality, intensive care unit (ICU) transfer, returns post-discharge, PEP, and cholangitis rates were similar between cohorts. Conclusion: Performing ERCP under GA compared to CS resulted in an increase in procedural success rates. Other complication rates were similar between groups.

Oats (Avena strigosa) as winter forage for dairy cows in Vietnam: an on-farm study.

In North Vietnam, during winter, alternative forage resources are needed to balance the feed ration of dairy cows. The objective of this study was to investigate the effect of oat forage as a component of traditional winter roughage diets on feed intake, milk production and feeding cost in dairy cows. The study was conducted on-farm using 24 mid-lactation Holstein-Friesian cows. The feeding experiment consisted of two successive periods and two dietary treatments per period. Traditional basal diets included fresh tropical grasses, maize silage and hay. The oat forage had no effect on the dry matter intake of the basal diet, but the total crude protein intake was higher in cows fed with oat diets than in those fed with control diets. The yield of butterfat-corrected milk (FCM) was not significantly different between diets during period 1, but there was a trend (P = 0.078) of higher FCM yields in cows fed with the oat diet compared to those with control diet during period 2 (17.3 vs. 16.3 kg/day). The decline rate in milk yield was significantly higher (P < 0.001) in cows fed with control diets than in those fed with oat diets in both experimental periods. The total feeding cost of cows fed with oat diets was on average 12 % lower than those fed with control diets (P < 0.01). So, the oat forage is an important winter resource for cows in North Vietnam allowing higher milk yield whilst reducing feeding cost, compared to traditional roughage diets.

Cellular morphine tolerance produced by ßarrestin-2-dependent impairment of µ-opioid receptor resensitization.

Chronic morphine treatment produces behavioral and cellular opioid tolerance that has been proposed to be caused by attenuated µ-opioid receptor (MOR) recovery from desensitization (resensitization). The process of MOR resensitization is thought to require ßarrestin-2 (ßarr-2)-dependent trafficking of desensitized receptors to endosomal compartments, followed by recycling of resensitized receptors back to the plasma membrane. However, there is little direct evidence for this, particularly in native neurons. This study used whole-cell patch-clamp recording in locus ceruleus (LC) neurons from wild-type (w.t.) and ßarr-2 knock-out (k.o.) mice to examine whether ßarr-2/dynamin-dependent trafficking is required for MOR resensitization in neurons from opioid-naive and morphine-treated mice. Surprisingly, recovery of MOR from acute desensitization in LC neurons does not require ßarr-2- or dynamin-dependent trafficking. To the contrary, MOR resensitization was accelerated by disruption of either ßarr-2 or dynamin function. Chronic morphine treatment caused cellular MOR tolerance and concurrently impaired MOR resensitization in neurons from w.t. mice, as expected from previous studies, but neither occurred in neurons from ßarr-2 k.o. mice. Moreover, the impairment of MOR resensitization caused by chronic morphine was reversed in w.t. neurons when G-protein-coupled receptor kinase-2 (GRK2) or dynamin function was disrupted. Together, these results establish that ßarr-2/dynamin-dependent receptor regulation is not required for MOR resensitization in LC neurons. Furthermore, chronic morphine treatment modifies GRK2-ßarr-2-dynamin-dependent MOR trafficking to impair receptor resensitization, thereby contributing to opioid tolerance in LC neurons by reducing the number of functional receptors on the surface membrane.

Prolonged stimulation of µ-opioid receptors produces ß-arrestin-2-mediated heterologous desensitization of α(2)-adrenoceptor function in locus ceruleus neurons.

Prolonged agonist stimulation of the µ-opioid receptor (MOR) initiates receptor regulatory events that rapidly attenuate receptor-mediated signaling (homologous desensitization). Emerging evidence suggests that persistent MOR stimulation can also reduce responsiveness of effectors to other G-protein-coupled receptors, termed heterologous desensitization. However, the mechanisms by which heterologous desensitization is triggered by MOR stimulation are unclear. This study used whole-cell patch-clamp recordings of ligand activated G-protein-activated inwardly rectifying potassium channel currents in mouse brain slices containing locus ceruleus (LC) neurons to determine the effects of prolonged stimulation of MOR on α(2)-adrenoceptor (α(2)-AR) function. The results show distinct and sequential development of homologous and heterologous desensitization during persistent stimulation of MOR in LC neurons with Met(5)-enkephalin (ME). ME stimulation of MOR promoted rapid homologous desensitization that reached a steady state after 5 min and partially recovered over 30 min. Longer stimulation of MOR (10 min) induced heterologous desensitization of α(2)-AR function that exhibited slower recovery than homologous desensitization. Heterologous (but not homologous) desensitization required ß-arrestin-2 (ßarr-2) because it was nearly abolished in ßarr-2-knockout (ko) mice. Heterologous (but not homologous) desensitization was also prevented by inhibition of ERK1/2 and c-Src signaling in wild-type (wt) mouse LC neurons. Heterologous desensitization may be physiologically relevant during exposure to high doses of opioids because α(2)-AR-mediated slow inhibitory postsynaptic currents were depressed in wt but not ßarr-2 ko LC neurons after prolonged exposure to opioids. Together, these findings demonstrate a novel mechanism by which ßarr-2 can regulate postsynaptic responsiveness to neurotransmitter release.

Management model for assessment of nitrogen flow from feed to pig manure after storage in Vietnam.

Nitrogen (N) losses from pig production and the recycling of N from manure to crops can harm the atmosphere, soil and ground water quality. This study intended to build a dynamic management model, adapted to the Vietnamese context, that links the N flow at all stages along the manure management chain from the N in the diets fed to grower-finisher pigs to the application of the manure in the field. The model assesses N contents and losses at each stage of manure management so that application of manure N can be adjusted to ensure optimal fertilizer value, while at the same time minimizing environmental damage. This model provides a tool for examining the N flow on pig farms, to adjust the N content of feeds, the pig population, and to minimize N discharge and emissions. The model is developed using Powersim software and data from feed-excretion, storage and composting experiments. For validation and performance of the model we used sub-datasets from feed-excretion experiments in Denmark and Vietnam that were not used to parameterize in the model. This article presents the development of the model and trial of the model through scenario analyses of pig production in livestock production zones. The objective is that policy makers, extension officers or agricultural advisors will use the model as a support management tool to formulate and adjust manure management practices. This includes assessment of the land carrying capacity in existing livestock production areas and of maximum acceptable manure loads in planned livestock production zones.

Two distinct mechanisms mediate acute mu-opioid receptor desensitization in native neurons.

Sustained stimulation of G-protein coupled receptors (GPCRs) leads to rapid loss of receptor function (acute desensitization). For many GPCRs including the mu-opioid receptor (MOR), an accepted mechanism for acute desensitization is through G-protein coupled receptor kinase (GRKs) mediated phosphorylation of the receptor, which facilitates the binding of beta-arrestins (betaarrs) to the receptor and then promotes endocytosis. However, the mechanism(s) that mediate acute desensitization have not yet been well defined in native neurons. This study used whole-cell patch clamp recording of G-protein coupled inward-rectifying potassium (GIRK) currents to assay MOR function and identify mechanisms of acute MOR desensitization in locus ceruleus (LC) neurons. The rate and extent of MOR desensitization were unaffected by beta(arr)-2 knock-out. Disruption of GRK2 function via inhibitory peptide introduced directly into neurons also failed to affect desensitization in wild type or beta(arr)-2 knock-outs. Inhibition of ERK1/2 activation alone had little effect on acute desensitization. However, when both GRK2-beta(arr)-2 and ERK1/2 functions were disrupted simultaneously, desensitization of MOR was nearly abolished. Together, these results suggest that acute desensitization of MOR in native LC neurons is determined by at least two molecular pathways, one involving GRK2 and beta(arr)2, and a parallel pathway mediated by activated ERK1/2.

Davalintide (AC2307), a novel amylin-mimetic peptide: enhanced pharmacological properties over native amylin to reduce food intake and body weight.

OBJECTIVE: The current set of studies describe the in vivo metabolic actions of the novel amylin-mimetic peptide davalintide (AC2307) in rodents and compares these effects with those of the native peptide. RESEARCH DESIGN AND METHODS: The anti-obesity effects of davalintide were examined after intraperitoneal injection or sustained peripheral infusion through subcutaneously implanted osmotic pumps. The effect of davalintide on food intake after lesioning of the area postrema (AP) and neuronal activation as measured by c-Fos, were also investigated. RESULTS: Similar to amylin, davalintide bound with high affinity to amylin, calcitonin and calcitonin gene-related peptide receptors. Acutely, davalintide displayed greater suppression of dark-cycle feeding and an extended duration of action compared with amylin (23 versus 6 h). Davalintide had no effect on locomotor activity or kaolin consumption at doses that decreased food intake. Davalintide-induced weight loss through infusion was dose dependent, durable up to 8 weeks, fat-specific and lean-sparing, and was associated with a shift in food preference away from high-fat (palatable) chow. Metabolic rate was maintained during active weight loss. Both davalintide and amylin failed to suppress food intake after lesioning of the AP and activated similar brain nuclei, with davalintide displaying an extended duration of c-Fos expression compared with amylin (8 versus 2 h). CONCLUSION: Davalintide displayed enhanced in vivo metabolic activity over amylin while retaining the beneficial properties possessed by the native molecule. In vitro receptor binding, c-Fos expression and AP lesion studies suggest that the metabolic actions of davalintide and amylin occur through activation of similar neuronal pathways.

Neural regulation of acetylcholinesterase mRNAs at mammalian neuromuscular synapses.

We examined the role of innervation on acetylcholinesterase (AChE) gene expression within mammalian skeletal muscle fibers. First, we showed the selective accumulation of AChE mRNAs within the junctional vs extrajunctional sarcoplasm of adult muscle fibers using a quantitative reverse transcription PCR assay and demonstrated by in situ hybridization experiments that AChE transcripts are concentrated immediately beneath the postsynaptic membrane of the neuromuscular junction. Next, we determined the influence of nerve-evoked activity vs putative trophic factors on the synaptic accumulation of AChE mRNA levels in muscle fibers paralyzed by either surgical denervation or selective blockage of nerve action potentials with chronic superfusion of tetrodotoxin. Our results indicated that muscle paralysis leads to a marked decrease in AChE transcripts from the postsynaptic sarcoplasm, yet the extent of this decrease is less pronounced after tetrodotoxin inactivation than after denervation. These results suggest that although nerve-evoked activity per se appears a key regulator of AChE mRNA levels, the integrity of the synaptic structure or the release of putative trophic factors contribute to maintaining the synaptic accumulation of AChE transcripts at adult neuromuscular synapses. Furthermore, the pronounced downregulation of AChE transcripts in paralyzed muscles stands in sharp contrast to the well-documented increase in nicotinic acetylcholine receptor mRNAs under these conditions, and indicates that expression of the genes encoding these two synaptic proteins are subjected to different regulatory mechanisms in adult muscle fibers in vivo.

OpenPET: A Flexible Electronics System for Radiotracer Imaging.

We present the design for OpenPET, an electronics readout system designed for prototype radiotracer imaging instruments. The critical requirements are that it has sufficient performance, channel count, channel density, and power consumption to service a complete camera, and yet be simple, flexible, and customizable enough to be used with almost any detector or camera design. An important feature of this system is that each analog input is processed independently. Each input can be configured to accept signals of either polarity as well as either differential or ground referenced signals. Each signal is digitized by a continuously sampled ADC, which is processed by an FPGA to extract pulse height information. A leading edge discriminator creates a timing edge that is "time stamped" by a TDC implemented inside the FPGA. This digital information from each channel is sent to an FPGA that services 16 analog channels, and information from multiple channels is processed by this FPGA to perform logic for crystal lookup, DOI calculation, calibration, etc. As all of this processing is controlled by firmware and software, it can be modified / customized easily. The system is open source, meaning that all technical data (specifications, schematics and board layout files, source code, and instructions) will be publicly available.

Naked mole rats activate neuroprotective proteins during hypoxia.

Naked mole rats are a long-lived animal model that age much like humans, but that can also withstand oxidative damage, cancer, neurodegenerative diseases, and severe hypoxic conditions, which is of particular interest to this study. The conditions of their underground burrows result in competition for oxygen consumption, yet despite this oxygen deprivation they emerge unscathed. To understand the mechanisms in place to facilitate neuronal preservation during hypoxia, we investigated the protein levels of well-known cell-stress factors. We found that under hypoxic conditions, nearly half of the proteins measured increased expression in brain, while only a few decreased. Under hypoxic conditions there appeared to be a HIF1α-centered response, where HIF1α and its interactors carbonic anhydrase 9, CITED2, p21/CIP1, and NFκB1, among others, were upregulated. Concurrently, a hypoxia-induced decrease of cytochrome c was consistent with decreased mitochondrial function and protection from apoptosis. The picture that emerges is one of neuroprotection, cell-cycle arrest, and the promotion of antiapoptotic functions, all of which are consistent with conserving energy and maintaining neural integrity under low oxygen levels. These results suggest how this species may be poised to face hypoxia and contribute to its remarkable ability to deal with myriad of other damaging factors and sets the stage for future work on the neuroprotective facilitators we identified.