A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.

The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.

Extreme bradycardia and tachycardia in the world's largest animal.

The biology of the blue whale has long fascinated physiologists because of the animal's extreme size. Despite high energetic demands from a large body, low mass-specific metabolic rates are likely powered by low heart rates. Diving bradycardia should slow blood oxygen depletion and enhance dive time available for foraging at depth. However, blue whales exhibit a high-cost feeding mechanism, lunge feeding, whereby large volumes of prey-laden water are intermittently engulfed and filtered during dives. This paradox of such a large, slowly beating heart and the high cost of lunge feeding represents a unique test of our understanding of cardiac function, hemodynamics, and physiological limits to body size. Here, we used an electrocardiogram (ECG)-depth recorder tag to measure blue whale heart rates during foraging dives as deep as 184 m and as long as 16.5 min. Heart rates during dives were typically 4 to 8 beats min-1 (bpm) and as low as 2 bpm, while after-dive surface heart rates were 25 to 37 bpm, near the estimated maximum heart rate possible. Despite extreme bradycardia, we recorded a 2.5-fold increase above diving heart rate minima during the powered ascent phase of feeding lunges followed by a gradual decrease of heart rate during the prolonged glide as engulfed water is filtered. These heart rate dynamics explain the unique hemodynamic design in rorqual whales consisting of a large-diameter, highly compliant, elastic aortic arch that allows the aorta to accommodate blood ejected by the heart and maintain blood flow during the long and variable pauses between heartbeats.

Lunge filter feeding biomechanics constrain rorqual foraging ecology across scale.

Fundamental scaling relationships influence the physiology of vital rates, which in turn shape the ecology and evolution of organisms. For diving mammals, benefits conferred by large body size include reduced transport costs and enhanced breath-holding capacity, thereby increasing overall foraging efficiency. Rorqual whales feed by engulfing a large mass of prey-laden water at high speed and filtering it through baleen plates. However, as engulfment capacity increases with body length (engulfment volume∝body length3.57), the surface area of the baleen filter does not increase proportionally (baleen area∝body length1.82), and thus the filtration time of larger rorquals predictably increases as the baleen surface area must filter a disproportionally large amount of water. We predicted that filtration time should scale with body length to the power of 1.75 (filter time∝body length1.75). We tested this hypothesis on four rorqual species using multi-sensor tags with corresponding unoccupied aircraft systems-based body length estimates. We found that filter time scales with body length to the power of 1.79 (95% CI: 1.61-1.97). This result highlights a scale-dependent trade-off between engulfment capacity and baleen area that creates a biomechanical constraint to foraging through increased filtration time. Consequently, larger whales must target high-density prey patches commensurate to the gulp size to meet their increased energetic demands. If these optimal patches are absent, larger rorquals may experience reduced foraging efficiency compared with smaller whales if they do not match their engulfment capacity to the size of targeted prey aggregations.

The feeling of the story: Narrating to regulate anger and sadness.

Admonitions to tell one's story in order to feel better reflect the belief that narrative is an effective emotion regulation tool. The present studies evaluate the effectiveness of narrative for regulating sadness and anger, and provide quantitative comparisons of narrative with distraction, reappraisal, and reexposure. The results for sadness (n = 93) and anger (n = 89) reveal that narrative is effective at down-regulating negative emotions, particularly when narratives place events in the past tense and include positive emotions. The results suggest that if people tell the "right" kind of story about their experiences, narrative reduces emotional distress linked to those experiences.

Phase I study of capecitabine combined with radioembolization using yttrium-90 resin microspheres (SIR-Spheres) in patients with advanced cancer.

BACKGROUND: This was a prospective single-centre, phase I study to document the maximum tolerated dose (MTD), dose-limiting toxicity (DLT), and the recommended phase II dose for future study of capecitabine in combination with radioembolization. METHODS: Patients with advanced unresectable liver-dominant cancer were enrolled in a 3+3 design with escalating doses of capecitabine (375-1000 mg/m(2) b.i.d.) for 14 days every 21 days. Radioembolization with (90)Y-resin microspheres was administered using a sequential lobar approach with two cycles of capecitabine. RESULTS: Twenty-four patients (17 colorectal) were enrolled. The MTD was not reached. Haematologic events were generally mild. Common grade 1/2 non-haematologic toxicities included transient transaminitis/alkaline phosphatase elevation (9 (37.5%) patients), nausea (9 (37.5%)), abdominal pain (7 (29.0%)), fatigue (7 (29.0%)), and hand-foot syndrome or rash/desquamation (7 (29.0%)). One patient experienced a partial gastric antral perforation with a capecitabine dose of 750 mg/m(2). The best response was partial response in four (16.7%) patients, stable disease in 17 (70.8%) and progression in three (12.5%). Median time to progression and overall survival of the metastatic colorectal cancer cohort was 6.4 and 8.1 months, respectively. CONCLUSIONS: This combined modality treatment was generally well tolerated with encouraging clinical activity. Capecitabine 1000 mg/m(2) b.i.d. is recommended for phase II study with sequential lobar radioembolization.

When is meaning making unhealthy for the self? The roles of neuroticism, implicit theories, and memory telling in trauma and transgression memories.

The aim of this study was to examine how three factors-neuroticism, implicit theories of personality, and memory telling-relate to patterns of healthy and unhealthy meaning making in two kinds of negative memories: traumas and transgressions. Healthy meaning making was defined as self-growth, whereas unhealthy meaning making was defined as viewing the self as damaged in traumas (damaged self) and as a bad person in transgressions (bad self). A total of 85 adult participants completed survey measures of personality and memory telling (retrospective reports of extent to which memory was shared with others) and wrote a narrative of a trauma and a transgression which were coded for specific forms of meaning making. Results revealed distinct patterns of associations for trauma and transgression memories. The combination of low neuroticism and an incremental theory (belief that personality can change) predicted self-growth in traumas, whereas memory telling was predictive of self-growth in transgressions, especially among incremental theorists. For unhealthy forms of meaning making, an entity theory (belief that personality is fixed) was associated with the bad self in transgressions, and viewing the self as damaged by traumas was more common among younger adults than older adults.

Acoustic signalling and behaviour of Antarctic minke whales (Balaenoptera bonaerensis).

Acoustic signalling is the predominant form of communication among cetaceans. Understanding the behavioural state of calling individuals can provide insights into the specific function of sound production; in turn, this information can aid the evaluation of passive monitoring datasets to estimate species presence, density, and behaviour. Antarctic minke whales are the most numerous baleen whale species in the Southern Ocean. However, our knowledge of their vocal behaviour is limited. Using, to our knowledge, the first animal-borne audio-video documentation of underwater behaviour in this species, we characterize Antarctic minke whale sound production and evaluate the association between acoustic behaviour, foraging behaviour, diel patterns and the presence of close conspecifics. In addition to the previously described downsweep call, we find evidence of three novel calls not previously described in their vocal repertoire. Overall, these signals displayed peak frequencies between 90 and 175 Hz and ranged from 0.2 to 0.8 s on average (90% duration). Additionally, each of the four call types was associated with measured behavioural and environmental parameters. Our results represent a significant advancement in understanding of the life history of this species and improve our capacity to acoustically monitor minke whales in a rapidly changing Antarctic region.

To reason or not to reason: is autobiographical reasoning always beneficial?

Autobiographical reasoning has been found to be a critical process in identity development; however, the authors suggest that existing research shows that such reasoning may not always be critical to another important outcome: well-being. The authors describe characteristics of people such as personality and age, contexts such as conversations, and experiences such as transgressions, which may hinder adaptive reasoning. They also propose alternatives to autobiographical reasoning for managing challenging events and constructing the life story, which include different kinds of meaning-making than those primarily focused on in the current literature.

Rorqual Lunge-Feeding Energetics Near and Away from the Kinematic Threshold of Optimal Efficiency.

Humpback and blue whales are large baleen-bearing cetaceans, which use a unique prey-acquisition strategy-lunge feeding-to engulf entire patches of large plankton or schools of forage fish and the water in which they are embedded. Dynamically, and while foraging on krill, lunge-feeding incurs metabolic expenditures estimated at up to 20.0 MJ. Because of prey abundance and its capture in bulk, lunge feeding is carried out at high acquired-to-expended energy ratios of up to 30 at the largest body sizes (∼27 m). We use bio-logging tag data and the work-energy theorem to show that when krill-feeding at depth while using a wide range of prey approach swimming speeds (2-5 m/s), rorquals generate significant and widely varying metabolic power output during engulfment, typically ranging from 10 to 50 times the basal metabolic rate of land mammals. At equal prey field density, such output variations lower their feeding efficiency two- to three-fold at high foraging speeds, thereby allowing slow and smaller rorquals to feed more efficiently than fast and larger rorquals. The analysis also shows how the slowest speeds of harvest so far measured may be connected to the biomechanics of the buccal cavity and the prey's ability to collectively avoid engulfment. Such minimal speeds are important as they generate the most efficient lunges. Sommaire Les rorquals à bosse et rorquals bleus sont des baleines à fanons qui utilisent une technique d'alimentation unique impliquant une approche avec élan pour engouffrer de larges quantités de plancton et bancs de petits poissons, ainsi que la masse d'eau dans laquelle ces proies sont situés. Du point de vue de la dynamique, et durant l'approche et engouffrement de krill, leurs dépenses énergétiques sont estimées jusqu'à 20.0 MJ. À cause de l'abondance de leurs proies et capture en masse, cette technique d'alimentation est effectuée à des rapports d'efficacité énergétique (acquise -versus- dépensée) estimés aux environs de 30 dans le cas des plus grandes baleines (27 m). Nous utilisons les données recueillies par des capteurs de bio-enregistrement ainsi que le théorème reliant l'énergie à l'effort pour démontrer comment les rorquals s'alimentant sur le krill à grandes profondeurs, et à des vitesses variant entre 2 et 5 m/s, maintiennent des taux de dépenses énergétiques entre 10 et 50 fois le taux métabolique basal des mammifères terrestres. À densités de proies égales, ces variations d'énergie utilisée peuvent réduire le rapport d'efficacité énergétique par des facteurs entre 2x et 3x, donc permettant aux petits et plus lents rorquals de chasser avec une efficacité comparable à celle des rorquals les plus grands et rapides. Notre analyse démontre aussi comment des vitesses d'approche plus lentes peuvent être reliées à la biomécanique de leur poche ventrale extensible, et à l'habilitée des proies à éviter d'être engouffrer. Ces minimums de vitesses sont importants car ils permettent une alimentation plus efficace énergétiquement.

Monocytic Maturation Induced by FLT3 Inhibitor Therapy of Acute Myeloid Leukemia: Morphologic and Immunophenotypic Characteristics.

BACKGROUND: FMS-like tyrosine kinase-3 (FLT3-ITD) mutations are some of the most common mutations in acute myeloid leukemia (AML), and patient outcomes have improved since the advent of tyrosine kinase inhibitors. First, granulocytic differentiation was described in FLT3-positive AML treated with FLT3 inhibitors, and more recently, monocytic differentiation was reported. METHODS: Two patients with myelomonocytic cells in their bone marrow were identified during routine follow-up after AML treatment that included FLT3 inhibitors. The bone marrow study was done as standard of care. RESULTS: Both patients had FLT3-ITD+ AML and showed an atypical maturing monocytic cell population and a decrease in the leukemic blast cell population after FLT3 inhibitor therapy. Concurrent genetic testing revealed persistent genetic abnormalities. CONCLUSIONS: These cases illustrate monocytic maturation in FLT3+ AML after FLT3 inhibitor treatment. It is critical for pathologists and clinicians to be aware of the differentiation phenomenon, as these patients have persistent molecular abnormalities despite response to treatment and normalization of blast counts.

A comparison of baleen whale density estimates derived from overlapping satellite imagery and a shipborne survey.

As whales recover from commercial exploitation, they are increasing in abundance in habitats that they have been absent from for decades. However, studying the recovery and habitat use patterns of whales, particularly in remote and inaccessible regions, frequently poses logistical and economic challenges. Here we trial a new approach for measuring whale density in a remote area, using Very-High-Resolution WorldView-3 satellite imagery. This approach has capacity to provide sightings data to complement and assist traditional sightings surveys. We compare at-sea whale density estimates to estimates derived from satellite imagery collected at a similar time, and use suction-cup archival logger data to make an adjustment for surface availability. We demonstrate that satellite imagery can provide useful data on whale occurrence and density. Densities, when unadjusted for surface availability are shown to be considerably lower than those estimated by the ship survey. However, adjusted for surface availability and weather conditions (0.13 whales per km2, CV = 0.38), they fall within an order of magnitude of those derived by traditional line-transect estimates (0.33 whales per km2, CV = 0.09). Satellite surveys represent an exciting development for high-resolution image-based cetacean observation at sea, particularly in inaccessible regions, presenting opportunities for ongoing and future research.

Use of Hartmann's procedure in England.

INTRODUCTION: Hartmann's procedure is widely used in the management of complicated diverticular disease and for colorectal cancer. Very little national data are available about the reasons for performing this procedure and the reversal rate. METHOD: Hospital episode statistics data were obtained from The Department of Health and exported to an Access database for analysis. A cohort of patients who underwent a Hartmann's procedure between April 2001 and March 2002 were identified and followed until April 2006 to identify patients undergoing reversal of Hartmann's. RESULTS: Approximately 3950 Hartmann's procedures were performed between April 2001 and March 2002, 2853 as an emergency and 1097 as an elective procedure. Most emergency Hartmann's were performed for benign disease (2067, 72.5%) whereas a majority of the elective Hartmann's were performed for cancer (756, 68.9%). Seven hundred and thirty six (23.3%) of these patients underwent reversal during the study period. The median time interval between a Hartmann's procedure and reversal was 284.5 days (interquartile range 181-468.25). CONCLUSION: This study represents the single largest cohort in whom outcome after Hartmann's procedure has been studied. A majority of Hartmann's are performed as an emergency for benign diseases and most of them are not reversed.

Body Flexibility Enhances Maneuverability in the World's Largest Predator.

Blue whales are often characterized as highly stable, open-ocean swimmers who sacrifice maneuverability for long-distance cruising performance. However, recent studies have revealed that blue whales actually exhibit surprisingly complex underwater behaviors, yet little is known about the performance and control of these maneuvers. Here, we use multi-sensor biologgers equipped with cameras to quantify the locomotor dynamics and the movement of the control surfaces used by foraging blue whales. Our results revealed that simple maneuvers (rolls, turns, and pitch changes) are performed using distinct combinations of control and power provided by the flippers, the flukes, and bending of the body, while complex trajectories are structured by combining sequences of simple maneuvers. Furthermore, blue whales improve their turning performance by using complex banked turns to take advantage of their substantial dorso-ventral flexibility. These results illustrate the important role body flexibility plays in enhancing control and performance of maneuvers, even in the largest of animals. The use of the body to supplement the performance of the hydrodynamically active surfaces may represent a new mechanism in the control of aquatic locomotion.

Why whales are big but not bigger: Physiological drivers and ecological limits in the age of ocean giants.

The largest animals are marine filter feeders, but the underlying mechanism of their large size remains unexplained. We measured feeding performance and prey quality to demonstrate how whale gigantism is driven by the interplay of prey abundance and harvesting mechanisms that increase prey capture rates and energy intake. The foraging efficiency of toothed whales that feed on single prey is constrained by the abundance of large prey, whereas filter-feeding baleen whales seasonally exploit vast swarms of small prey at high efficiencies. Given temporally and spatially aggregated prey, filter feeding provides an evolutionary pathway to extremes in body size that are not available to lineages that must feed on one prey at a time. Maximum size in filter feeders is likely constrained by prey availability across space and time.

Using Digital Tags With Integrated Video and Inertial Sensors to Study Moving Morphology and Associated Function in Large Aquatic Vertebrates.

The anatomy of large cetaceans has been well documented, mostly through dissection of dead specimens. However, the difficulty of studying the world's largest animals in their natural environment means the functions of anatomical structures must be inferred. Recently, non-invasive tracking devices have been developed that measure body position and orientation, thereby enabling the detailed reconstruction of underwater trajectories. The addition of cameras to the whale-borne tags allows the sensor data to be matched with real-time observations of how whales use their morphological structures, such as flukes, flippers, feeding apparatuses, and blowholes for the physiological functions of locomotion, feeding, and breathing. Here, we describe a new tag design with integrated video and inertial sensors and how it can be used to provide insights to the function of whale anatomy. This technology has the potential to facilitate a wide range of discoveries and comparative studies, but many challenges remain to increase the resolution and applicability of the data. Anat Rec, 300:1935-1941, 2017. © 2017 Wiley Periodicals, Inc.

How Baleen Whales Feed: The Biomechanics of Engulfment and Filtration.

Baleen whales are gigantic obligate filter feeders that exploit aggregations of small-bodied prey in littoral, epipelagic, and mesopelagic ecosystems. At the extreme of maximum body size observed among mammals, baleen whales exhibit a unique combination of high overall energetic demands and low mass-specific metabolic rates. As a result, most baleen whale species have evolved filter-feeding mechanisms and foraging strategies that take advantage of seasonally abundant yet patchily and ephemerally distributed prey resources. New methodologies consisting of multi-sensor tags, active acoustic prey mapping, and hydrodynamic modeling have revolutionized our ability to study the physiology and ecology of baleen whale feeding mechanisms. Here, we review the current state of the field by exploring several hypotheses that aim to explain how baleen whales feed. Despite significant advances, major questions remain about the processes that underlie these extreme feeding mechanisms, which enabled the evolution of the largest animals of all time.

Regulating Emotion and Identity by Narrating Harm.

This study examined how narration of harm experiences can regulate self and emotions in ways relevant to well-being. Participants (n = 88, 65% female) were asked to provide 6 narratives about instances when they were victims of harm and 6 narratives about instances when they were perpetrators of harm. Narratives were coded for extent of exploration, growth, damage conclusions and resolution. Participants drew damage conclusions more frequently in victim narratives and growth conclusions more frequently in perpetrator narratives. Both the type of experience (victim or perpetrator) and the way the experience was narrated (references to damage conclusions and resolution) predicted emotion and identity implications, which were, in turn, related to well-being. Implications for narrative approaches to self-regulation are discussed.

Congenital central hypoventilation and sleep state.

Congenital central hypoventilation (Ondine's curse) is described in an infant with persistant symptoms throughout the first nine months of life. Respiratory control was most severely affected in quiet sleep, although abnormalities were present in rapid eye movement (REM) sleep and while awake. Failure of metabolic control in quiet sleep led to profound hypoventilation. Behavioral or "behavioral-like" inputs in the awake state and REM sleep increased ventilation, but not to expected normal levels. The ventilatory response to inhaled 4% CO2 was markedly depressed in all states.

Surgical epicardial ablation of left ventricular pathway using sling exposure.

We report our experience with 43 consecutive patients with left free wall pathways operated on since December 1988 using a modified direct epicardial approach through a medial sternotomy, without the adjunct of normothermic cardiopulmonary bypass. The left atrioventricular sulcus is exposed by dislocating the heart cephalad and to the right using a sling made of a large sponge passed around the ventricle through the transverse sinus. While the arterial pressure is monitored, the heart is positioned to obtain adequate exposure without compromising the ventricular function. The left atrioventricular junction is exposed using a direct approach. The epicardium is incised along the ventricular edge and a plane of dissection is identified and opened using blunt dissection over the ventricular wall. The entire left atrioventricular junction can be exposed. After dissection, electrophysiological testing is repeated to assess accessory pathway conduction. Epicardial cryoablation was used when accessory pathway conduction was not present (42 patients). Transmural cryoablation was used under normothermic cardiopulmonary bypass when accessory pathway conduction persisted after dissection (subendocardial pathway). In all, cardiopulmonary bypass was not used in 41 patients. There was one early relapse that required transmural cryoablation. There were no complications.

False family history of breast cancer in the family cancer clinic.

AIMS: Awareness of hereditary breast and ovarian cancer in both the general public and the medical profession is increasing. Individuals who may be at risk on the basis of a family history are requesting risk determination and appropriate management in a variety of settings. Risk determination relies largely on pedigree analysis and epidemiological data. METHODS: We describe five individuals presenting in the family cancer or genetic counselling clinic where a factitious family or personal history led to erroneous risk estimation. Common factors in these families are a history of benign breast disease, poor communication within families, long survival with early onset or bilateral disease, a lack of detailed knowledge of the illness and treatment in close relatives and inconsistencies in the history in repeated consultations.