bluuebunny/crossref_metadata_2025 huggingface dataset:
Passot-Type Immediate Breast Reconstruction Obviates the Use of Aceullular Dermal Matrix in Grades 2 and 3 Ptosis
Authors: Rivet Joshua J. , Day Kristopher M. , Rau Jeffrey F. , Waldrop Jimmy L. , Brzezienski Mark A.
Published: January 2019

Purpose

Acellular dermal matrices (ADMs) are commonly used for immediate breast reconstruction after skin-sparing mastectomy (SSM). Regnault grades 2 and 3 ptotic breasts feature significant mastectomy flap redundancy that may be incorporated into the reconstruction. This allows surgeons to use patients' de-epithelialized inferior dermal pedicle instead of ADM.

Methods

All consecutive SSM patients with Regnault grade 2 or 3 ptosis who underwent Passot-type immediate breast reconstruction (IBBR) with tissue expanders (TEs) and de-epithelialized inferior dermal pedicle without an ADM were included. Patient data from the electronic medical record, clinical photographs, and a comparative cost analysis of ADM versus additional operative time are provided.

Results

Thirty-eight patients with an average age of 52.7 years, weight 210.5 lb, and body mass index of 35.1 kg/m2 were treated (34 bilateral, 4 unilateral; 72 reconstructed breasts). Average mastectomy specimens weighed 962.8 g. Tissue expanders were filled to 265.0 mL (41.6% capacity) intraoperatively, and final implant volume averaged 710.9 ± 118.5 mL after an average of 628.6 ± 74.1-mL expansion. Operative times for Passot-type IBBR was 124.3 ± 37.7 versus 92.5 ± 27.9 minutes (P = 0.0001) for submuscular TE placement with ADM. The operative technique is described in detail. There were 8 TE explantations (21.1%) included: intractable infection (10.5%; n = 4), symptomatic capsular contracture (7.9%; n = 3), and spontaneous TE deflation (2.6%; n = 1). All but 3 patients (92.1%) successfully completed Passot reconstruction, with 2 patients declining salvage latissimus dorsi flap reconstruction and 1 patient lost to follow-up. Total cost savings in this case series was $89,724 ($2361 ± $3529/case).

Conclusions

Additional prospective comparison studies are needed to determine whether Passot-type IBBR results in higher complication rates than conventional IBBR with ADM in this challenging patient population. Passot-type IBR after SSM is safe, demonstrates acceptable rates of successful breast reconstruction, confers cost savings by obviating the use of ADM, and provides favorable aesthetic results.
Alloplastic Cranioplasty Reconstruction
Authors: Oliver Jeremie D. , Banuelos Joseph , Abu-Ghname Amjed , Vyas Krishna S. , Sharaf Basel
Published: January 2019

Background

Acquired defects of the cranium represent a reconstructive challenge in patients with calvarial bone loss due to trauma, infection, neoplasia, congenital malformations, or other etiologies. The objective of this study was to compare postoperative rates of infection, local complications, and allograft failures following cranioplasty reconstruction using titanium mesh (Ti), polymethyl methacrylate (PMMA), polyether ether ketone (PEEK), and Norian implants in adult patients.

Methods

This constitutes the first systematic review of available literature on 4 different methods of alloplastic cranioplasty reconstruction, including Ti, PMMA, PEEK, and Norian implants, using the Newcastle-Ottawa Quality Assessment Scale guidelines for article identification, screening, eligibility, and inclusion. Electronic literature search included Ovid MEDLINE/PubMed, EMBASE, Scopus, Google Scholar, and Cochrane Database. Pearson exact test was utilized at P < 0.05 level of significance (J.M.P. v11 Statistical Software).

Results

A total of 53 studies and 3591 patients (mean age, 40.1 years) were included (Ti = 1429, PMMA = 1459, PEEK = 221, Norian = 482). Polymethyl methacrylate implants were associated with a significantly higher infection rate (7.95%, P = 0.0266) compared with all other implant types (6.05%). Polyether ether ketone implants were associated with a significantly higher local complication rate (17.19%, P = 0.0307, compared with 12.23% in all others) and the highest ultimate graft failure rate (8.60%, P = 0.0450) compared with all other implant types (5.52%).

Conclusions

This study qualifies as a preliminary analysis addressing the knowledge gap in rates of infection, local surgical complication, and graft failure in alloplastic cranioplasty reconstruction with different implant types in the adult population. Longer-term randomized trials are warranted to validate associations found in this study.
Can Head Circumference Be Used as a Proxy for Intracranial Volume in Patients With Craniosynostosis?
Authors: Hashmi Asra , Cahill Gabrielle L. , Zaldana Michelle , Davis Greta , Cronin Brendan J. , Brandel Michael G. , Beletsky Alexander , Taj Raeda , Buckstaff Taylor M. , Vinocur Daniel , Lance Samuel , Meltzer Hal S. , Gosman Amanda A.
Published: January 2019

Background

Calculation of intracranial volume from neuroimaging can be complex and time consuming. In the adult population, there is evidence suggesting that owing to its strong correlation, head circumference (HC) may be used as a surrogate for intracranial volume (ICV). We were interested in studying the correlation between HC and ICV in patients with craniosynostosis.

Methods

After institutional review board approval, a retrospective review was performed on patients with craniosynostosis. GE Healthcare AdW 4.3 volume assessment software was used to calculate ICV and HC based on preoperative computed tomographic scans. Pearson correlation was used to estimate correlation coefficients between ICV and HC for this patient population, with 0 to 0.3 considered a weak correlation, 0.4 to 0.6 considered a moderate correlation, 0.7 to 1 considered a strong correlation, andP< 0.05 was considered statistically significant.

Results

A total of 196 craniosynostosis patients were included in this study. There were 121 male and 75 female patients. Seventy-nine patients had metopic, 45 had coronal, 64 had sagittal, and 8 had lambdoid synostosis. Mean age was 8.2 months. Mean HC and ICV were 42.9 cm and 829 cm3, respectively. Overall, there was a strong correlation between HC and ICV (r= 0.81). Patients were further categorized by craniosynostosis type. Very strong correlation was obtained for patients with coronal (0.89), metopic (0.98), and lambdoid craniosynostosis (0.97). Strong correlation was obtained for patients with sagittal synostosis (0.73). When categorized by sex, a stronger correlation was obtained for female patients (0.84) compared with male patients (0.80). Statistical significance was reached for all reported correlations.

Conclusion

Our preliminary data suggest that a very strong correlation exists between HC and ICV for male and female patients with all types of craniosynostosis, making HC a useful surrogate for ICV in this patient population.
National Surgical Quality Improvement Program Analysis of 9110 Reduction Mammaplasty Patients
Authors: Young Zachary T. , Close Michaela , Herrera Fernando A.
Published: January 2019

Background

The purpose of this study was to identify preoperative risk factors in patients undergoing reduction mammoplasty as well as identify any increased complication risk in patients older than 60 years undergoing reduction mammoplasty.

Methods

The American College of Surgeons National Surgical Quality Improvement Program data from years 2013–2015 was reviewed. Patients were identified using Current Procedural Terminology code 19318 specific for reduction mammoplasty. Only patients undergoing bilateral procedures were included, and no reconstructive procedures were included. Patient demographics, comorbidities, and 30-day complications were analyzed. Comparative analysis was performed between patients younger than 60 years and patients 60 years and older, identifying risk factors associated with complications in the geriatric population.

Results

A total of 9110 patients undergoing reduction mammoplasty were identified. Of these 1442 (15.83%) were patients older than 60 years. Mean age of all patients was 42 years (range, 18–85 years). Eighty hundred fifty-nine patients were active smokers. Four hundred eighty-two patients were diabetic. Overall, 798 complications occurred with an incidence of 8.7%. Group 1 (<60 years) mean age was 39 years (range, 18–59). Group 2 (>60 years) mean age was 66 years (range, 60–85 years). The geriatric population showed a higher risk of cerebral vascular accidents (P < 0.00006), myocardial infarction (P < 0.02), and readmission (P < 0.03). Smoking was found to be a statistically significant risk factor for superficial surgical site infection, and deep space infection. Diabetes was found to be a statistically significant risk factor for readmission.

Conclusions

Reduction mammoplasty is a common surgical procedure. It is not uncommon for patients older than 60 years to undergo elective reduction mammoplasty (15.83% incidence), resulting in a cumulative complication rate of 11.65% in the geriatric population compared with 8.89% in the group of patients younger than 60 years. Smoking and diabetes were found to be independent risk factors for complications, regardless of age.
Regional Anesthetic Blocks in Plastic Surgery Using Portable Ultrasound
Authors: Homsy Christopher , Lindsey John T.
Published: January 2019

Background

With the introduction of latest generation ultrasound technology and its easy availability and portability, regional anesthetic blocks, which were formally in the domain of anesthesiologists, have now become available to practicing plastic surgeons. Enhanced Recovery After Surgery protocols for other specialties such as orthopedics and colorectal surgery have incorporated regional anesthetic blocks. These regional blocks have been shown to be effective in improving the patient comfort and experience and decreasing reliance on opioid medications.

Methods

Patients scheduled for elective plastic surgery received PEC-1, serratus anterior plane, or transversus abdominis plane blocks as indicated for the proposed procedure. All blocks were performed under ultrasound guidance using the Philips Lumify system with the linear array 12-4 probe by the operating surgeon.

Results

A total of 83 patients received regional anesthetic blocks by the senior author. Thirty-three patients undergoing cosmetic breast augmentation or implant-based breast reconstruction received the PEC-1 and the serratus anterior plane blocks after the induction of anesthesia but before the prep and drape. Fifty patients undergoing either abdominoplasty or deep inferior epigastric perforator flap reconstruction received intraoperative transversus abdominis plane blocks. Anatomic planes were clearly visualized with this new ultrasound technology. Patients experienced good to excellent analgesia with less reliance on opioid medications and decreased need for refills. For hospitalized patients, length of stay in some cases was decreased up to 1 day, and PCA pumps were eliminated. There were no complications or adverse sequelae observed in any of these patients related to the regional blocks.

Conclusions

Incorporation of these known regional anesthetic techniques in this single-surgeon experience seems to confirm reports of effectiveness in the anesthesia literature and may be of benefit to a wide range of plastic surgery patients.
Factors Associated With Complications in Immediate Breast Reconstruction in 1 Stage With Completely Submuscular Implants
Authors: Yazar Sukru , Altinkaya Altug , Bengur Fuat Baris , Karadag Emine Cigdem , Kara Halil , Uras Cihan
Published: January 2019

Background

Immediate breast reconstruction in 1 stage using permanent implants is gaining popularity and can be performed with or without the use of acellular dermal matrices. This study aimed to investigate the results of breast implants placed submuscularly without acellular dermal matrix and assess the factors affecting surgical complications.

Methods

From November 2009 to March 2018, 138 patients underwent immediate breast reconstruction with permanent submuscular implants after concomitant skin-sparing or nipple-sparing mastectomies in a single institution. All implants were covered with sufficient soft tissue under a submuscular pocket.

Results

One hundred thirty-eight patients were enrolled, and a total of 196 breasts were operated. The average age and body mass index (BMI) of the patients were 44.9 ± 8.8 years and 23.7 ± 3.6 kg/m2, respectively. The majority of the mastectomies were therapeutic (81%). The average volume of implants was 389 ± 89 mL, and the mean follow-up was 33 months. The overall complication rate was 17% (n = 23), with skin necrosis being the most common complication followed by infections. Having a BMI equal to or greater than 25 kg/m2 was found to be a statistically significant predictor for overall complications (P = 0.002), whereas smoking history, age, and implant volume were not statistically significant.

Conclusions

Immediate breast reconstruction in 1 stage using permanent implants can be performed with acceptable complication rates and cosmetic outcomes. Our study demonstrated that high BMI is a risk factor for overall complications. With proper patient selection and surgical technique, implants could be completely covered under a submuscular pocket.
Lipopolysaccharide Stress Induces Cryptic Exon Splice Variants of the Human Glucocorticoid Receptor
Authors: Green Tajia L. , Leventhal Stacey M. , Lim Debora , Cho Kiho , Greenhalgh David G.
Published: January 2019

Glucocorticoids are widely used in the treatment of numerous inflammatory conditions, including sepsis. Unfortunately, patient response to glucocorticoid therapy can be inconsistent. Variations in the human glucocorticoid receptor (hGR) may contribute to the differential patient response. We screened for hGR variants in the buffy coats of burn patients and peripheral blood mononuclear cells (PBMCs) treated with lipopolysaccharide. Three novel splice variants containing cryptic exons were upregulated in the PBMCs after lipopolysaccharide exposure at 3 and 13 h with the greatest observed expression at 3 h. Luciferase assays revealed that two of the isoforms had no significant activity in comparison with the reference hGR when stimulated with hydrocortisone. The third isoform had an augmented response that was greater than the reference hGR at a high cortisol dose. This shows that PBMCs are able to produce variant hGR isoforms in response to stress. Furthermore, lipopolysaccharide stress appears to induce these hGR variants, potentially by influencing mRNA splicing. In the future, identifying hGR expression profiles may be a key component in individually tailoring a patient's treatment to sepsis and injury.
Cannabinoid therapy in epilepsy
Authors: Billakota Santoshi , Devinsky Orrin , Marsh Eric
Published: January 2019

Purpose of review

To review the history, pharmacology, and clinical science of cannabidiol (CBD) in the treatment of epilepsy.

Recent findings

Phase III randomized controlled trials and prospective open label trials have provided efficacy and safety data for the use of CBD in pediatric onset severe epilepsies. The product that was studied in the vast majority of these published trials, Epidiolex (>99% of CBD and <0.10% Δ9-tetrahydrocannabinol (THC); GW pharmaceuticals, Cambridge, UK), has now been FDA approved based on this published data.

Identification of CBD, Δ9-THC, and the endocannabinoid system in the mid-20th century has led to advancement of cannabis-based therapies for epilepsy. Based on clinical trial data, Epidiolex is the first CBD medication approved by a national regulatory agency (US Food and Drug Administration for Dravet and Lennox Gastaut syndrome). Approval of CBD as a treatment for these rare and severe pediatric-onset epilepsy syndromes is an important milestone, but the complete spectrum of use of cannabis-derived products, and the use of CBD for other epilepsy syndromes remains to be determined.
Neurological profiles beyond the sleep disorder in patients with anti-IgLON5 disease
Authors: Gaig Carles , Compta Yaroslau
Published: January 2019

Purpose of review

Anti-IgLON5 disease is a novel entity characterized by a distinctive sleep disorder associated with a variety of neurological symptoms, antibodies against IgLON5, and pathological findings of neuronal tauopathy. The characteristic sleep disorder occurs in most patients, but other neurological symptoms are also important because they can be the presenting and most disabling problem and mimic other conditions. This review focuses on nonsleep neurological symptoms and presentations of anti-IgLON5 disease.

Recent findings

Apart from sleep problems, the most frequent neurological symptoms in anti-IgLON5 disease are bulbar dysfunction and gait abnormalities. Other symptoms include movement disorders like chorea or abnormal orofacial movements, oculomotor abnormalities, cognitive impairment, and symptoms of nervous system hyperexcitability. All these symptoms can present in different combinations and severity leading to distinct clinical phenotypes beyond the sleep disorder: bulbar syndrome; syndrome resembling progressive supranuclear palsy; cognitive impairment, sometimes with chorea, mimicking Huntington disease; gait ataxia; and stiff-person-like syndrome.

These clinical presentations may suggest degenerative or other neurological disorders, but anti-IgLON5 disease has to be considered, and confirmed by the detection of IgLON5 antibodies, when the criteria for the diagnosis of the initially suspected disorders are not fulfilled, confirmatory laboratory tests are negative, and significant sleep problems are present.
Clinical and EEG Characteristics of Ifosfamide-Related Encephalopathy
Authors: Gusdon Aaron M. , Malani Rachna , Chen Xi
Published: January 2019

Purpose:

Ifosfamide can lead to a syndrome of central nervous system toxicity. Here, we investigate the clinical and EEG characteristics of patients with ifosfamide-related encephalopathy.

Methods:

Retrospective data were collected on patients from Memorial Sloan Kettering Cancer Center, who developed encephalopathy associated with ifosfamide between 2007 and 2017. Patients who had an EEG performed were included. Clinical and laboratory data were retrospectively collected. Each EEG recording was reviewed and compared with the originally documented EEG report.

Results:

Sixteen patients with ifosfamide-related encephalopathy were included, with primary tumors consisting of lymphoma (N = 9), sarcoma (N = 4), poorly differentiated ovarian cancer (N = 1), neuroblastoma (N = 1), and papillary serous adenocarcinoma (N = 1). Laboratory results ruled out other etiologies of encephalopathy. Generalized periodic discharges with or without triphasic morphology were seen most commonly (N = 9), with a distinct pattern of interspersed intermittent background attenuation seen in five patients. Background slowing and intermittent rhythmic delta activity (N = 4), bursts of bilateral synchronized delta activity (N = 2), and frontal predominant intermittent delta activity (N = 1) were also seen. One patient demonstrated a pattern consistent with nonconvulsive status epilepticus. Although most patients experienced resolution of symptoms, those who died demonstrated a variety of EEG abnormalities. Abnormal movements were common, with six patients demonstrating characteristic orofacial myoclonus.

Conclusions:

Ifosfamide-related encephalopathy commonly results in a distinct pattern of generalized periodic discharges admixed with intermittent background attenuation on EEG. Abnormal movements, in particular orofacial myoclonus, are also common. Recognizing these clinical and EEG features might lead to early detection of ifosfamide-related encephalopathy.
Area Under the Curve of Somatosensory Evoked Potentials Detects Spinal Cord Injury
Authors: Jorge Ahmed , Zhou James , Dixon Edward C. , Hamilton Kojo D. , Balzer Jeffrey , Thirumala Parthasarathy
Published: January 2019

Purpose:

Intraoperative neurophysiological monitoring using somatosensory evoked potentials has been linked to a reduction in the incidence of neurological deficits during corrective surgery. Nonetheless, quantitative assessments of somatosensory evoked potential waveforms are often difficult to evaluate, because they are affected by anesthesia, injury, and noise. Here, we discuss a novel method that integrates somatosensory evoked potential signals into a single metric by calculating the area under the curve (AUC).

Methodology:

Thirty-two Sprague-Dawley rats underwent a laminectomy procedure and were then randomly assigned to a control group or to receive a contusive spinal cord injury ranging from 100 to 200 kilodynes. Neurophysiological testing was completed at various points perioperatively and postoperatively. Somatosensory evoked potential traces obtained were processed and the AUC metric was calculated.

Results:

The AUC significantly decreased to 11% of its baseline value after impact and remained at 25% baseline after 1 hour for the 200-kdyn cohort. Postimpact, AUC for the control versus the 150-kdyn and 200-kdyn groups, and the 150-kdyn versus 200-kdyn groups were significantly higher (P < 0.01, P < 0.001, and P < 0.05, respectively). Across days, the only significant parameter accounting for AUC variability was impact force, P < 0.0001 (subject parameters and number of days were not significant).

Conclusions:

The AUC metric can detect an iatrogenic contusive spinal cord injury immediately after its occurrence. Moreover, this metric can detect different iatrogenic injury impact force levels and identify injury in the postoperative period. The AUC integrates multiple Intraoperative neurophysiological monitoring measures into a single metric and thus has the potential to help clinicians and investigators evaluate spinal cord impact injury status.
Replicated evolutionary inhibition of a complex ancestral behaviour in an adaptive radiation
Authors: Foster Susan A. , O'Neil Shannon , King Richard W. , Baker John A.
Published: January 2019

Adaptive radiations often exhibit high levels of phenotypic replication, a phenomenon that can be explained by selection on standing variation in repeatedly divergent environments or by the influence of ancestral plasticity on selection in divergent environments. Here, we offer the first evidence that plastic loss of expression of a complex display in a novel environment, followed by selection against expression, could lead to replicated evolutionary inhibition of the phenotype. In both ancestral (oceanic) and benthic (freshwater) populations of the threespine stickleback fish, cannibalism is common and males defending nests respond to approaching groups with a complex diversionary display. This display is not exhibited by males in allopatric, limnetic (freshwater) populations from which cannibalistic groups are absent. Laboratory-reared males from three limnetic populations exhibit a reduced tendency to respond to cannibalistic foraging groups relative to laboratory-reared ancestral and benthic males, but still are capable of producing a similar array of forms of the display despite many generations of disuse. Thus, replication in adaptive radiations can reflect reduced expression of an ancestral trait followed by evolutionary inhibition while the population retains the capacity to express the trait under extreme ancestral conditions.
Hierarchical architecture of spider attachment setae reconstructed from scanning nanofocus X-ray diffraction data
Authors: Schaber Clemens F. , Flenner Silja , Glisovic Anja , Krasnov Igor , Rosenthal Martin , Stieglitz Hergen , Krywka Christina , Burghammer Manfred , Müller Martin , Gorb Stanislav N.
Published: January 2019

When sitting and walking, the feet of wandering spiders reversibly attach to many surfaces without the use of gluey secretions. Responsible for the spiders' dry adhesion are the hairy attachment pads that are built of specially shaped cuticular hairs (setae) equipped with approximately 1 µm wide and 20 nm thick plate-like contact elements (spatulae) facing the substrate. Using synchrotron-based scanning nanofocus X-ray diffraction methods, combining wide-angle X-ray diffraction/scattering and small-angle X-ray scattering, allowed substantial quantitative information to be gained about the structure and materials of these fibrous adhesive structures with 200 nm resolution. The fibre diffraction patterns showed the crystalline chitin chains oriented along the long axis of the attachment setae and increased intensity of the chitin signal dorsally within the seta shaft. The small-angle scattering signals clearly indicated an angular shift by approximately 80° of the microtrich structures that branch off the bulk hair shaft and end as the adhesive contact elements in the tip region of the seta. The results reveal the specific structural arrangement and distribution of the chitin fibres within the attachment hair's cuticle preventing material failure by tensile reinforcement and proper distribution of stresses that arise upon attachment and detachment.
Improving the propulsion speed of a heaving wing through artificial evolution of shape
Authors: Ramananarivo Sophie , Mitchel Thomas , Ristroph Leif
Published: January 2019

Aeronautical studies have shown that subtle changes in aerofoil shape substantially alter aerodynamic forces during fixed-wing flight. The link between shape and performance for flapping locomotion involves distinct mechanisms associated with the complex flows and unsteady motions of an air- or hydro-foil. Here, we use an evolutionary scheme to modify the cross-sectional shape and iteratively improve the speed of three-dimensional printed heaving foils in forward flight. In this algorithmic-experimental method, ‘genes’ are mathematical parameters that define the shape, ‘breeding’ is the combination of genes from parent wings to form a daughter, and a wing's measured speed is its ‘fitness’ that dictates its likelihood of breeding. Repeated over many generations, this process automatically discovers a fastest foil whose cross-section resembles a slender teardrop. We conduct an analysis that uses the larger population to identify what features of this shape are most critical, implicating slenderness, location of maximum thickness and fore-aft asymmetries in edge sharpness or bluntness. This analysis also reveals a tendency towards extremely thin and cusp-like trailing edges. These findings demonstrate artificial evolution in laboratory experiments as a successful strategy for tailoring shape to improve propulsive performance. Such a method could be used in related optimization problems, such as tuning kinematics or flexibility for flapping propulsion, and for flow–structure interactions more generally.
Butyricimonas faecalis sp. nov., isolated from human faeces and emended description of the genus Butyricimonas
Authors: Le Roy Tiphaine , Van der Smissen Patrick , Paquot Adrien , Delzenne Nathalie , Muccioli Giulio G. , Collet Jean-François , Cani Patrice D.
Published: January 2019

A Gram-negative, strictly anaerobic, non-spore forming, non-motile, non-pigmented bacterial strain, designated H184T, was isolated from human faeces. 16S rRNA gene sequence analysis showed that strain H184T represents a member of the genus

Butyricimonas

. Strain H184T is related to but distinct from

Butyricimonas

virosa

JCM 15149T and

Butyricimonas

paravirosa

JCM 18677T, with 16S rRNA gene sequence similarities of 96.32 and 96.24 %, respectively. Strain H184T shared 90.50 % hsp60 gene sequence similarity to B.

virosa

JCM 15149T and

B. paravirosa

JCM 18677T. Growth occurs between 25 and 42 °C with an optimum at 37 °C. Bile and NaCl concentration range allowing growth are 0–3.75 % and 0–1.8 %, respectively. pH range for growth is 5.5–8. The strain produced propionate as the major end product from glucose. The major cellular fatty acids of strain H184T were iso-C15 : 0 (63.5 %) and iso-C17 : 0 3-OH (12.8%). The major menaquinone of the strain was MK-10 (86 %). DNA G+C content of the isolate H184T was 44.2 mol%. The genome-based comparison between strain H184T and

B. virosa

JCM 15149T by pairwise average nucleotide identity indicated a clear distinction with a score of 87.22. On the basis of these data, strain H184T represents a novel species of the genus

Butyricimonas

, for which the name

Butyricimonas
faecalis sp. nov. is proposed. The type strain of B. faecalis is H184T (DSM 106867T, LMG 30602T).
Galton-Watson Process and Bayesian Inference: A Turnkey Method for the Viability Study of Small Populations
Authors: Cloez B. , Daufresne T. , Kerioui M. , Fontez B.
Published: January 2019

Sharp prediction of extinction times is needed in biodiversity monitoring and conservation management.

The Galton-Watson process is a classical stochastic model for describing population dynamics. Its evolution is like the matrix population model where offspring numbers are random. Extinction probability, extinction time, abundance are well known and given by explicit formulas. In contrast with the deterministic model, it can be applied to small populations.

Parameters of this model can be estimated through the Bayesian inference framework. This enables to consider nonarbitrary scenarios.

We show how coupling Bayesian inference with the Galton-Watson model provides several features: i) a flexible modelling approach with easily understandable parameters ii) compatibility with the classical matrix population model (Leslie type model) iii) A non-computational approach which then leads to more information with less computing iv) a non-arbitrary choice for scenarios, parameters… It can be seen to go one step further than the classical matrix population model for the viability problem.

To illustrate these features, we provide analysis details for two examples whose one of which is a real life example.
A fruitful endeavor: scent cues and echolocation behavior used by Carollia castanea to find fruit
Authors: Leiser-Miller Leith B. , Kaliszewska Zofia A. , Lauterbur M. Elise , Mann Brianna , Riffell Jeffrey A. , Santana Sharlene E.
Published: January 2019

Frugivores have evolved sensory and behavioral adaptations that allow them to find ripe fruit effectively, but the relative importance of different senses in varying foraging scenarios is poorly known. Within Neotropical ecosystems, short-tailed fruit bats (Carollia: Phyllostomidae) are abundant nocturnal frugivores, relying primarily on plants of the genus Piper as a food resource. Previous research has demonstrated Carollia employ olfaction and echolocation to locate Piper fruit, but it is unknown how their sensory use and foraging decisions are influenced by the complex diversity of chemical cues that fruiting plants produce. Using wild C. castanea and their preferred food, Piper scintillans, we conducted behavioral experiments to test two main hypotheses: (1) foraging decisions in C. castanea are primarily driven by ripe fruit scent and secondarily by vegetation scent, and (2) C. castanea re-weight their sensory inputs to account for available environmental cues, such that bats rely more heavily on echolocation in the absence of adequate scent cues. Our results suggest that C. castanea requires olfactory information and relies almost exclusively on ripe fruit scent to make foraging attempts. Ripe fruit scent is chemically distinct from vegetation scent in P. scintillans, with a greater abundance of β-caryophyllene, germacrene D and β-elemene, and a few unique compounds. Although variation in echolocation call parameters was independent of scent cue presence, bats emitted longer and more frequent echolocation calls in trials where no fruit scent was present. Altogether, these results highlight the adaptations, plasticity, and potential constraints in the sensory system of neotropical fruit bats.

SIGNIFICANCE STATEMENT

Little is known about the relative importance of different senses and which plant cues are most important for fruit location by frugivores. We conducted behavioral experiments on short-tailed fruit bats (Carollia castanea), which use a combination of olfaction and echolocation to find ripe fruit, and their preferred food source (Piper scintillans) to test (1) which plant scent cues drive food selection and (2) if bats alter their echolocation behaviors based on which scent cues are present. We find that C. castanea rely almost exclusively on ripe fruit scent to forage, and echolocate more frequently when fruit scent is absent. Ripe fruit scent is chemically different from vegetation scent in P. scintillans, potentially providing a clear signal of food availability to mutualistic bats. These results highlight the sensory adaptations and behavioral flexibility of fruit bats as they navigate the cues provided by fruiting plants.
Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica
Authors: Zhang Fen , Li Wei , Gao Cheng-wen , Gao Li-zhi
Published: January 2019

Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. Despite its enormous industrial, cultural and medicinal values, the chloroplast (cp) and mitochondrial (mt) genomes are not available for Camellia sinensis var. assamica. In this study, we de novo assembled the cp genome sequence of C. sinensis var. assamica into a circular contig of 157,100 bp in length with an overall GC content of 37.29%, comprising a large single-copy region (LSC, 86,649 bp) and a small single-copy region (SSC, 18,285 bp) separated by a pair of inverted repeats (IRs, 26,083 bp). We annotated a total of 141 cp genes, of which 87 are protein-coding genes, 46 are tRNA genes, and eight are rRNA genes. We also de novo assembled the mt genome of C. sinensis var. assamica into two complete circular scaffolds (702,253 bp and 178,082 bp) with overall GC contents of 45.63% and 45.81%, respectively. We annotated a total of 71 mt genes, including 44 protein-coding genes, 24 tRNAs, and 3 rRNAs. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ∼4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an invaluable resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.
Genotypic frequencies at equilibrium for polysomic inheritance under double-reduction
Authors: Huang Kang , Wang Tongcheng , Dunn Derek W. , Zhang Pei , Cao Xiaoxiao , Liu Rucong , Li Baoguo
Published: January 2019

Polyploids are organisms whose genomes consist of more than two complete sets of chromosomes. Both autopolyploids and allopolyploids may display polysomic inheritance. A peculiarity of polysomic inheritance is multivalent formation during meiosis resulting in double-reduction, which occurs when sister chromatid fragments are segregated into the same gamete. Double-reduction can result in gametes carrying identical-by-descent alleles and slightly increasing homozygosity. This will cause the genotypic frequencies to deviate from expected values and will thus bias the results of standard population genetic analytical methods used in molecular ecology and selective breeding. In this study, we extend existing double-reduction models to account for any even level of ploidy, and derive the symbolic expressions for genotypic frequencies via two methods. Inbreeding coefficients and heterozygosity under double-reduction and inbreeding are also calculated. Numerical solutions obtained by computer simulations are compared with analytical solutions predicted by the model to validate the model.
Is it time to change the reference genome?
Authors: Ballouz Sara , Dobin Alexander , Gillis Jesse
Published: January 2019

The use of the human reference genome has shaped methods and data across modern genomics. This has offered many benefits while creating a few constraints. In the following piece, we outline the history, properties, and pitfalls of the current human reference genome. In a few illustrative analyses, we focus on its use for variant-calling, highlighting its nearness to a “type specimen”. We suggest that switching to a consensus reference offers important advantages over the current reference with few disadvantages.
Gene sharing networks to automate genome-based prokaryotic viral taxonomy
Authors: Jang Ho Bin , Bolduc Benjamin , Zablocki Olivier , Kuhn Jens H. , Roux Simon , Adriaenssens Evelien M. , Brister J. Rodney , Kropinski Andrew M , Krupovic Mart , Turner Dann , Sullivan Matthew B.
Published: January 2019

Viruses of bacteria and archaea are likely to be critical to all natural, engineered and human ecosystems, and yet their study is hampered by the lack of a universal or scalable taxonomic framework. Here, we introduce vConTACT 2.0, a network-based application to establish prokaryotic virus taxonomy that scales to thousands of uncultivated virus genomes, and integrates confidence scores for all taxonomic predictions. Performance tests using vConTACT 2.0 demonstrate near-identical correspondence to the current official viral taxonomy (>85% genus-rank assignments at 96% accuracy) through an integrated distance-based hierarchical clustering approach. Beyond “known viruses”, we used vConTACT 2.0 to automatically assign 1,364 previously unclassified reference viruses to tentative taxa, and scaled it to modern metagenomic datasets for which the reference network was robust to adding 16,000 viral contigs. Together these efforts provide a systematic reference network and an accurate, scalable taxonomic analysis tool that is critically needed for the research community.
The hidden costs of dietary restriction: implications for its evolutionary and mechanistic origins
Authors: McCracken Andrew W , Adams Gracie , Hartshorne Laura , Simons Mirre J. P.
Published: January 2019

Dietary restriction (DR) consistently and universally extends health-and lifespan across taxa. Despite efforts to uncover the mechanisms underpinning DR - and ultimately translate its beneficial outcomes to humans - precise and universal mechanisms have not been identified. In biomedical science, the effects of DR are interpreted as regulating pro-longevity molecular pathways. This reasoning is guided by the conviction that DR evolved as an adaptive, pro-longevity physiological response to restricted food intake. Current evolutionary theory states that organisms should invest in their soma more heavily during periods of DR, and, when their resource availability improves, should outcompete age-matched rich-fed controls in survival and/or reproduction. Here we present a formal test of these key predictions utilising a large-scale demographic approach detailing mortality and fecundity in Drosophila melanogaster fed alternating dietary regimes (N > 66,000 flies across 11 genetic lines). Our experiments reveal surprising and substantial mortality costs when returning to a rich diet after periods of DR. These results suggest the effects of DR are not necessarily intrinsically pro-longevity and could be considered an escape from costs incurred under nutrient-rich conditions, in addition to novel, discrete costs associated with restricting dietary protein. These insights question the relevance of current evolutionary explanations of DR in interpreting the mechanistic basis of dietary restriction.
Interplay of pericentromeric genome organization and chromatin landscape regulates the expression ofDrosophila melanogasterheterochromatic genes
Authors: Saha Parna , Sowpati Divya Tej , Srivastava Ishanee , Mishra Rakesh Kumar
Published: January 2019

Transcription of heterochromatic genes residing within the constitutive heterochromatin is paradoxical to the tenets of the epigenetic code.Drosophila melanogasterheterochromatic genes serve as an excellent model system to understand the mechanisms of their transcriptional regulation. Recent developments in chromatin conformation techniques have revealed that genome organization regulates the transcriptional outputs. Thus, using 5C-seq in S2 cells, we present a detailed characterization of the hierarchical genome organization ofDrosophilapericentromeric heterochromatin and its contribution to heterochromatic gene expression. We show that pericentromeric TAD borders are enriched in nuclear Matrix attachment regions while the intra-TAD interactions are mediated by various insulator binding proteins. Heterochromatic genes of similar expression levels cluster into Het TADs which indicates their transcriptional co-regulation. To elucidate how heterochromatic factors, influence the expression of heterochromatic genes, we performed 5C-seq in the HP1a or Su(var)3-9 depleted cells. HP1a or Su(var)3-9 RNAi results in perturbation of global pericentromeric TAD organization but the expression of the heterochromatic genes is minimally affected. Subset of active heterochromatic genes have been shown to have combination of HP1a/H3K9me3 with H3K36me3 at their exons. Interestingly, the knock-down of dMES-4 (H3K36 methyltransferase), downregulates expression of the heterochromatic genes. This indicates that the local chromatin interactions and the combination of heterochromatic factors (HP1a or H3K9me3) along with the H3K36me3 is crucial to drive the expression of heterochromatic genes. Furthermore, dADD1, present near the TSS of the active heterochromatic genes, can bind to both H3K9me3 or HP1a and facilitate the heterochromatic gene expression by regulating the H3K36me3 levels. Therefore, our findings provide mechanistic insights into the interplay of genome organization and chromatin factors at the pericentromeric heterochromatin that regulatesDrosophila melanogasterheterochromatic gene expression.
Fear in dreams and in wakefulness: evidence for day/night affective homeostasis
Authors: Sterpenich V , Perogamvros L , Tononi G , Schwartz S
Published: January 2019

Despite partial experimental evidence, it is a long-standing and common belief that dreams serve an emotion regulation function. Revisiting this idea, recent neuroscientific theories have proposed that emotions experienced in dreams contribute to the resolution of emotional distress (e.g. fear extinction) and preparation for future waking affective reactions. Here we addressed one emerging common prediction from these theoretical accounts, namely that experiencing fear in dreams is associated with more adapted responses to threatening signals during wakefulness. Using a stepwise approach across two studies, we first identified brain regions activated when experiencing fear in dreams and then showed that frightening dreams modulated the response of these same regions to threatening stimuli during wakefulness. As predicted, more fear in dreams was associated with reduced activation of those fear-responsive regions during wakefulness. Specifically, in Study 1, we performed serial awakenings in 18 participants recorded throughout the night with high-density EEG and asked them whether they experienced any fear in their dreams. Insula activity increased (i.e. decreased delta and increased gamma power) for dreams containing fear. In Study 2, we tested 89 participants and found that those with higher incidence of fear in their dreams showed reduced fMRI response to fear-eliciting stimuli in the insula, amygdala and midcingulate cortex, while awake. Consistent with better emotion regulation processes, the same participants also displayed increased medial prefrontal cortex activity. These findings support that emotions in dreams and wakefulness engage similar neural substrates, and substantiate a link between emotional processes occurring during sleep and emotional brain functions during wakefulness.
Development of new food-sharing relationships among nonkin vampire bats
Authors: Carter Gerald G. , Farine Damien R. , Crisp Rachel J. , Vrtilek Julia K. , Ripperger Simon P. , Page Rachel A.
Published: January 2019

In an individualized animal society, social bonds can foster cooperation and enhance survival and reproduction. Cooperative bonds often exist among kin, but nonkin can also develop high-investment cooperative bonds that share similarities with human friendship. How do such bonds form? One theory suggests that strangers should ‘test the waters’ of a new relationship by making small initial cooperative investments and gradually escalating them with good partners. This ‘raising-the-stakes’ strategy is demonstrated by human strangers in short-term economic games, but it remains unclear whether it applies to helping in a natural long-term social bond. Here we show evidence that unfamiliar vampire bats (Desmodus rotundus) selectively escalate low-cost investments in allogrooming before developing higher-cost food-sharing relationships. We introduced females from geographically distant sites in pairs or groups and observed that bats established new reciprocal grooming relationships, and that increasing grooming rates predicted the occurrence of first food donations, at which point grooming rates no longer increased. New food-sharing relationships emerged reciprocally in 14% of female pairs, typically over 10-15 months, and developed faster when strangers lacked alternative familiar partners. A gradual grooming-to-sharing transition among past strangers suggests that ‘raising the stakes’ might be more evident when tracking multiple cooperative behaviours as new relationships form, rather than measuring a single behavior in an established relationship. ‘Raising the stakes’ could play a similar underappreciated role across a broader spectrum of social decisions with long-term consequences, such as joining a new social group or forming a long-term pair-bond.

Significance statement

Vampire bats form long-term cooperative social bonds that involve reciprocal food sharing. How do two unrelated bats go from being strangers to having a high-investment food-sharing relationship? We introduced unfamiliar bats and found evidence that low-cost grooming paves the way for higher-cost food donations. Food sharing emerged in a reciprocal fashion and it emerged faster when two strangers did not have access to their original groupmates. The bats that formed new food-sharing relationships had a history of escalating reciprocal grooming up until the food sharing began. Our finding that unfamiliar nonkin vampire bats appear to gradually and selectively transition from low-cost to high-cost cooperative behaviors is the first evidence that nonhuman individuals ‘raise the stakes’ when forming new cooperative relationships.