bluuebunny/crossref_metadata_2025 huggingface dataset:
Relational Morphology in the Parallel Architecture
Authors: Jackendoff Ray , Audring Jenny
Published: January 2019

Relational Morphology is based in the mentalistic perspective of the Parallel Architecture (Jackendoff 2002). Morphology is the grammar of word-sized pieces of structure, comprising morphosyntax and its interfaces to phonology, semantics, and phrasal syntax. Many morphological patterns are nonproductive; their instances must be listed in the lexicon. They therefore resist formulation in terms of traditional procedural rules; declarative schemas prove more adequate. Productive schemas can build novel forms; nonproductive schemas cannot. Instead, they motivate relations among lexical items. Lexical relations are often described in terms of inheritance; this chapter proposes enrichments that render inheritance more adequate for morphology. Productive schemas too can motivate lexical relations. Hence they are just like nonproductive schemas except that they have ‘gone viral’. The authors conclude that the focus on productive patterns has deflected attention from a more basic issue: the architecture of the lexicon, the structure of lexical items, and the relationships among them.
Theoretical Issues in Inflection
Authors: Stump Gregory
Published: January 2019

The domains of divergence among current conceptions of inflectional morphology appertain to five fundamental issues. What are the basic units in terms of which inflectional morphology is defined? Is the morpheme a theoretically significant concept? What sort of structure do inflected word forms possess? Do they have a quasi-syntactic hierarchical structure that determines their semantic composition? What is the relation between concatenative and nonconcatenative inflectional patterns? Are they equivalent alternatives for realizing morphosyntactic content or is affixation pre-eminent, sometimes triggering nonconcatenative operations of secondary status? What is the relation between a word form’s morphosyntactic properties and their inflectional exponents? Are exponents lexically listed with their properties, or do a word form’s morphosyntactic properties trigger rules that specify their exponents? Finally, what distinguishes inflection from word formation? Are these discrete components? Is their difference purely one of function? Competing answers to these questions are examined in the light of empirical evidence.
The W-subtype active contact binary PZ UMa with a possible more massive tertiary component
Authors: Zhou Xiao , Soonthornthum Boonrucksar
Published: January 2019

Two sets of multiple-color (B, V, RC, IC) light curves of PZ UMa were observed independently with the 2.4 m telescope at the Thai National Observatory and the 1 m telescope at Yunnan Observatories. The light curves were analyzed with the Wilson–Devinney program and the two sets of light curves produced consistent results, which shows that PZ UMa is a W-subtype contact binary with an extreme mass ratio (M1/M2 = 0.18). The basic physical parameters of PZ UMa were determined to be M2 = 0.77(2) M⊙, M1 = 0.14(1) M⊙, R2 = 0.92(1) R⊙, R1 = 0.43(1) R⊙, L2 = 0.46(2) L⊙, and L1 = 0.15(3) L⊙. The orbital period analysis of PZ UMa revealed a 13.22 yr periodicity, which implies that there may be a tertiary component orbiting around the binary system. The mass and orbital radius of the tertiary component were calculated to be M3 = 0.88 M⊙ and a3 = 3.67 au, if the orbit was coplanar with the central binary system. It is interesting that the minimum mass of the tertiary was calculated to be M3min = 0.84 M⊙, which means the tertiary component is even larger than the primary star and the secondary one of PZ UMa. PZ UMa is a late-type contact binary with stellar activity. The O’Connell effect appeared on its light curves when it was observed in 2016 April. However, the O’Connell effect reversed when the target was observed again in 2016 December. The changes of the O’Connell effect on such a short time-scale strongly support the occurrence of rapidly changing magnetic activity in this W UMa binary.
Bangladesh Police in United Nations Peacekeeping Operations and Capacity Building: Striving for Perfection in an Imperfect World!
Authors: Zaman Rashed , Biswas Niloy
Published: January 2019

Since 1988, Bangladesh has been one of the highest police contributing countries (PCCs) to United Nations Peacekeeping operations. Over the years, Bangladesh Police has not only carved out space for itself as a top PCC, but also earned a name for itself as a dependable force which delivered the tasks assigned to it. However, in the last few years, Bangladesh Police has seen a fall in deployment to various missions due to an increasing number of participation of other new contributors across the world. Moreover, there are significant transformations in the nature of conflict and mandates of peacekeeping operations which would require Bangladesh Police to be prepared itself for future participation in such missions. Against such a backdrop, this article examines how Bangladeshi police peacekeepers evaluate their participation in peace missions and their capacity in addressing the challenges of the contemporary and future peace missions. It also investigates issues of capacity building, skill enhancement, and increasing competency of Bangladesh police peacekeepers as perceived by themselves. This article argues Bangladesh needs to comprehend the changing scenario and enhance the capacity of police peacekeepers by undertaking appropriate measures including tapping into the experience of its returning police personnel. Otherwise, the sustainability of Bangladesh’s participation in UN police peacekeeping deployments may face severe stress and become problematic.
Is It Relevant to Keep Advocating Visual Inspection of the Cervix With Acetic Acid for Primary Cervical Cancer Screening in Limited-Resource Settings?
Authors: Domgue Joel Fokom , Valea Fidel A.
Published: January 2019

(Abstracted from J Global Oncol 2018;(4):1–5)

The significant decline in incidence of cervical cancer in high-income settings is largely the result of the widespread use of human papillomavirus (HPV)–based cytology screening and vaccination programs. However, this preventable disease is one of the commonest and deadliest women's cancer in resource-poor developing countries and will remain so until high-impact primary interventions (including vaccination against HPV) are widely used and implemented.
The Rise and Fall of Mesh in Pelvic Surgery and the Shortcomings of Medical Device Regulation
Authors: Trabuco Emanuel C. , Montori Victor M.
Published: January 2019

(Abstracted from Obstet Gynecol 2018;132:736–740)

The introduction of tension-free vaginal tape (TVT) “sling” procedure revolutionized incontinence surgery. Rapid uptake of the TVT procedure led to its subsequent use in 90% of the annual incontinence surgeries performed in the United States.
Decreased Endothelial Function and Increased Subclinical Heart Failure in Women Several Years After Pre-eclampsia
Authors: Breetveld N. M. , Ghossein-Doha C. , van Neer J. , Sengers M. J. J. M. , Geerts L. , van Kuijk S. M. J. , van Dijk A. P. , van der Vlugt M. J. , Heidema W. M. , Brunner-la Rocca H. P. , Scholten R. R. , Spaanderman M. E. A.
Published: January 2019

(Abstracted from Ultrasound Obstet Gynecol 2018;52:196–204)

Preeclampsia (PE) is associated with both postpartum endothelial dysfunction and asymptomatic structural heart alterations consistent with heart failure stage B (HF-B). This study assessed the relationship between endothelial function, along with components of metabolic syndrome, and asymptomatic structural heart dysfunction in formerly preeclamptic women and healthy parous controls.
Wash, Rinse, Repeat: Which Patients Undergo Serial Joint Irrigation in Pediatric Septic Hip Arthritis?
Authors: Livingston Kristin S. , Kalish Leslie A. , Bae Donald S. , Kim Young-Jo , Shore Benjamin J.
Published: January 2019

Background:

The purpose of this study is to identify risk factors associated with repeat surgical irrigation in pediatric septic hip arthritis.

Methods:

A single center retrospective case-control study was performed. Patients who underwent ≥2 washouts (cases) were compared with those who had only 1 washout (controls). Demographic, clinical, laboratory, microbial, and magnetic resonance imaging data were compared between cases and controls and a prediction model was developed using logistic regression. A risk score was then constructed by counting the number of risk factors from the model that were present in each patient.

Results:

We identified 26 patients between 1994 and 2015 who underwent ≥2 washouts for septic hip arthritis, and 63 control patients who had only a single washout. Twenty-two patients had 2 washouts, 3 had 4 washouts, 1 had 5 washouts. Median number of days between first and second washout was 5 (interquartile range, 4 to 8). The most common reason for repeat washout was persistent fever (N=21), followed by persistently elevated laboratory values (N=13), abnormal magnetic resonance imaging findings (N=12), and continued pain (N=12). Repeat washout cases demonstrated higher temperature preoperatively (P<0.001), had more frequent initial misdiagnosis (P=0.002), and had a longer time from symptom onset to surgery (P=0.02). Laboratory values in these cases showed higher C-reactive protein (P=0.003), and more frequent left shift (P=0.03) at presentation, with a greater proportion of positive cultures (P<0.001). Postoperatively, repeat washout cases had higher temperatures (P<0.001), more frequent wound drainage (P=0.02), and complications (P=0.001). A risk score for predicting the likelihood of undergoing repeat washout was constructed by counting the number of the following factors present: presence of left shift in CBC, positive blood or synovial fluid cultures, and postoperative temperature over 39°C. Seventy percent of cases had ≥2 of these risk factors and 80% of controls had ≤1 risk factor.

Conclusions:

Cases of pediatric septic arthritis which undergo repeat washout are associated with left shift, high postoperative temperatures, and positive cultures. They have more frequent misdiagnosis leading to delayed treatment and subsequent medical complications.

Level of Evidence:

Level III.
Dimeglio Score Predicts Treatment Difficulty During Ponseti Casting for Isolated Clubfoot
Authors: Brazell Chris , Carry Patrick M. , Jones Alex , Baschal Robin , Miller Nancy , Holmes Kaley S. , Georgopoulos Gaia
Published: January 2019

Background:

The Dimeglio score (DS) is widely used to assess clubfoot severity, but its ability to predict long-term outcomes following Ponseti treated isolated clubfoot (IC) is controversial. This study tested the association between the initial DS and its individual parameters with the number of Ponseti clubfoot casts required to achieve correction and the rate of early recurrence following treatment.

Methods:

Data were retrospectively collected from patients who underwent treatment of IC between March 2012 and March 2015 and were followed for ≥2 years. DSs were collected at the initial casting visit. The number of Ponseti casts required to achieve clubfoot correction before tenotomy and recurrence of deformity were collected as the primary outcome variables. Recurrence was defined as any loss of correction leading to repeat casting or tenotomy during the bracing phase. Negative binomial and logistic regression analyses were used to test the association between the 8 Dimeglio parameters and number of casts and incidence of recurrence, respectively.

Results:

A total of 53 patients (37 male and 16 female) were included in the study. The median number of casts required to achieve an acceptable correction was 5 (range, 2 to 16). The incidence of recurrence was 24.53% (13/53). An increase in derotation, varus, equinus, muscle condition, and total DSs at the initial cast visit were associated with a significant (P<0.05) increase in the number of casts required to achieve an acceptable correction. The derotation parameter [rate ratio: 1.30, 95% confidence interval (CI): 1.13-1.50, P=0.0003] was most strongly associated with number of casts. Total DSs at initial visit was the only variable significantly associated with the incidence of deformity recurrence (odds ratio: 1.36, 95% confidence interval: 1.01-1.84, P=0.0482).

Conclusion:

Initial DS is correlated with the number of casts required for correction in Ponseti treated IC. DS may help physicians establish realistic expectations for families with regard to the length of treatment and the possibility of recurrence following Ponseti treatment.

Level of Evidence:

Level II—retrospective prognostic study.
Addressing the Needs of Transgender Patients: How Gynecologists Can Partner in Their Care
Authors: Dendrinos Melina L. , Budrys Nicole M. , Sangha Roopina
Published: January 2019

Importance

With the increase in patients who identify as transgender, it is crucial that gynecologists are culturally and clinically competent in understanding their unique needs.

Objective

The aim of this study was to identify the key gynecologic issues facing transgender patients and develop an overarching framework of tools needed to address these issues.

Evidence Acquisition

A review of the existing literature was undertaken to address the key clinical aspects of care.

Results

Various aspects of the gynecologic care of transgender patients, including health maintenance and cancer screening examinations, hormone replacement therapy, hysterectomy and salpingo-oophorectomy, and referral and collaboration with the patient's care team, are outlined.

Conclusions and Relevance

Transgender patients are more likely to be engaged and seek care if their identity and their needs are understood. While many aspects of transgender health care follow standard practices, there are significant and important differences, including gender-affirming therapies. This article aims to give gynecologists the necessary tools to partner in the care of transgender patients.

Target Audience

Obstetricians and gynecologists, family physicians.

Learning Objectives

After participating in this activity, physicians should be better able to define “transgender”; distinguish health risks unique to the transgender population and propose appropriate screening; differentiate criteria for starting hormone therapy and the regimens available for transgender men; assess gender-affirming surgery techniques; and compare fertility options with patients before and after transitioning.
Vitamin D Supplementation in Pregnancy and Lactation and Infant Growth
Authors: Roth Daniel E. , Morris Shaun K. , Zlotkin Stanley , Gernand Alison D. , Ahmed Tahmeed , Shanta Shaila S. , Papp Eszter , Korsiak Jill , Shi Joy , Islam M. Munirul , Jahan Ishrat , Keya Farhana K. , Willan Andrew R. , Weksberg Rosanna , Mohsin Minhazul , Rahman Qazi S. , Shah Prakesh S. , Murphy Kellie E. , Stimec Jennifer , Pell Lisa G. , Qamar Huma , Al Mahmud Abdullah
Published: January 2019

(Abstracted from N Engl J Med 2018;379:535–546)

It is unclear whether maternal vitamin D supplementation during pregnancy and lactation improves fetal and infant growth in regions where vitamin D deficiency is common.
Tranexamic Acid for the Prevention of Blood Loss After Vaginal Delivery
Authors: Sentilhes Loïc , Winer Norbert , Azria Elie , Sénat Marie-Victoire , Le Ray Camille , Vardon Delphine , Perrotin Franck , Desbrière Raoul , Fuchs Florent , Kayem Gilles , Ducarme Guillaume , Doret-Dion Muriel , Huissoud Cyril , Bohec Caroline , Deruelle Philippe , Darsonval Astrid , Chrétien Jean-Marie , Seco Aurélien , Daniel Valérie , Deneux-Tharaux Catherine
Published: January 2019

(Abstracted from N Engl J Med 2018;379:731–742)

The use of tranexamic acid (TXA) reduces mortality in the setting of postpartum hemorrhage (PPH). This study investigated whether the prophylactic administration of TXA in addition to prophylactic oxytocin in women with vaginal delivery would decrease the incidence of PPH.
Autologous Breast Reconstruction With the Latissimus Dorsi Muscle With Immediate Fat Grafting
Authors: Brondi Renata Suzuki , de Oliveira Vilmar Marques , Bagnoli Fábio , Mateus Evandro Falacci , Rinaldi José Francisco
Published: January 2019

Objective

The aim of this study was to describe a variation of the breast reconstruction technique with myocutaneous flap of the fat-grafted latissimus dorsi muscle and its outcomes and evaluation of patient satisfaction.

Method

This prospective cohort study included 18 patients and 19 reconstructed breasts, with 1 bilateral case. There were 7 cases of late reconstruction and 11 cases of immediate reconstruction. The flap was prepared with fat at the time of surgery, which was injected before its preparation. The evaluation of the results regarding shape, volume, and symmetry was performed through a satisfaction scale completed by patients and 2 physicians from 12 to 18 months after reconstruction.

Results

On average, 171.31 mL of fat was injected (100–275 mL); the average time of unilateral surgery was 3 hours 42 minutes (3 hours to 4 hours 30 minutes). After a mean follow-up of 26.38 months (13–38 months), we did not observe complications of this new technique. In the evaluation performed by patients regarding the shape, volume, and symmetry, more than 80% rated the outcome as excellent and good, and the evaluations by the medical team were also satisfactory. In the comparative analysis between immediate and late reconstruction, patients who underwent immediate reconstruction were more satisfied.

Conclusions

This reconstruction technique with autologous fat injection was effective, with satisfactory and long-lasting results, and without the requirement for implants to set breast shape and volume.
Pregnancy As a Risk Factor for Small Bowel Obstruction After Laparoscopic Gastric Bypass Surgery
Authors: Stenberg Erik , Chen Ruoqing , Hildén Karin , Fall Katja
Published: January 2019

Objective:

To evaluate whether pregnancy is associated with increased risk for small bowel obstruction after laparoscopic gastric bypass surgery.

Background:

Small bowel obstruction is a common and feared long-term complication to laparoscopic gastric bypass surgery that may be more common during pregnancy. It is unclear if the risk truly increases during pregnancy.

Methods:

Women, 18 to 55 years, operated with a primary laparoscopic gastric bypass procedure from 2010 until 2015 were identified through the Scandinavian Obesity Surgery Registry (n = 25,853). Through record-linkage to the Medical Birth Registry, the National Patient Registry, and review of hospital charts, information on pregnancy periods and outcome were obtained. The main outcome was operation due to small bowel obstruction after the laparoscopic gastric bypass procedure.

Results:

Pregnancy was associated with increased risk for small bowel obstruction following laparoscopic gastric bypass surgery (incidence rates 46.5, 95% CI 38.0–56.9/1000 person-years, vs 20.9 95% CI 19.9–22.0; adjusted-HR 1.72, 95% CI 1.39–2.12, P < 0.001). While no excess risk was observed during the first trimester, the second (adjusted-HR 1.67, 95% CI 1.17–2.39, P = 0.005) and third (adjusted-HR 2.69, 95% CI 2.02–3.59, P < 0.001) conferred increased risk. The incidence rate of small bowel obstruction during pregnancy was 42.9 (95% CI 32.4–57.0/1000 person-years) among women for whom the mesenteric defects had been closed during the primary procedure, and 53.2 (95% CI 38.9–72.8/1000 person-years) for women in whom they had been left open.

Conclusion:

Pregnancy is associated with increased risk for small bowel obstruction after laparoscopic gastric bypass surgery during the second and third trimesters.
Understanding the Costs Associated With Surgical Care Delivery in the Medicare Population
Authors: Kaye Deborah R. , Luckenbaugh Amy N. , Oerline Mary , Hollenbeck Brent K. , Herrel Lindsey A. , Dimick Justin B. , Hollingsworth John M.
Published: January 2019

Background:

Surgical care has been largely untargeted by Medicare payment reforms because episode costs associated with its delivery are not currently well understood.

Objective:

To quantify the costs of inpatient and outpatient surgery in the Medicare population.

Methods:

We analyzed claims data from a 20% national sample of Medicare beneficiaries (2008–2014). For a given study year, we identified all inpatient and outpatient procedures and constructed claims windows around them to define surgical episodes. After summing payments for services rendered during each episode, we totaled all inpatient and outpatient episode payments by surgical specialty. For inpatient episodes, we determined component payments related to the index hospitalization, readmissions, physician services, and postacute care. For outpatient episodes, we differentiated by the site of care (hospital outpatient department versus physician office versus ambulatory surgery center). We used linear regression to evaluate temporal trends in inpatient and outpatient surgical spending. Finally, we estimated the contribution of surgical care to overall Medicare expenditures.

Results:

Total Medicare payments for surgical care are substantial, representing 51% of Program spending in 2014. They declined modestly over the study period, from $133.1 billion in 2008 to $124.9 billion in 2014 (−6.2%, P = 0.085 for the temporal trend). While spending on inpatient surgery contributed the most to total surgical payments (69.4% in 2014), it declined over the study period, driven by decreases in index hospitalization (−16.7%, P = 0.002) and readmissions payments (−27.0%, P = 0.003). In contrast, spending on outpatient surgery increased by $8.5 billion (28.7%, P < 0.001). This increase was realized across all sites of care (hospital outpatient department: 36.6%, P < 0.001; physician office: 22.1%, P < 0.001; ambulatory surgery center: 36.6%, P < 0.001). Ophthalmology and hand surgery witnessed the greatest growth in surgical spending over the study period.

Conclusions and Relevance:

Surgical care accounts for half of all Medicare spending. Our findings not only highlight the magnitude of spending on surgery, but also the areas of greatest growth, which could be targeted by future payment reforms.
Opioid Prescription Patterns for Children Following Laparoscopic Appendectomy
Authors: Sonderman Kristin A. , Wolf Lindsey L. , Madenci Arin L. , Kwon Nicollette K. , Armstrong Lindsey B. , Wanis Kerollos Nashat , Taylor Kathryn , Uribe-Leitz Tarsicio , Koehlmoos Tracey P. , Ricca Robert L. , Weil Brent R. , Weldon Christopher B. , Haider Adil H. , Rice-Townsend Samuel E.
Published: January 2019

Objective:

To describe variability in and consequences of opioid prescriptions following pediatric laparoscopic appendectomy.

Summary Background Data:

Postoperative opioid prescribing patterns may contribute to persistent opioid use in both adults and children.

Methods:

We included children <18 years enrolled as dependents in the Military Health System Data Repository who underwent uncomplicated laparoscopic appendectomy (2006–2014). For the primary outcome of days of opioids prescribed, we evaluated associations with discharging service, standardized to the distribution of baseline covariates. Secondary outcomes included refill, Emergency Department (ED) visit for constipation, and ED visit for pain.

Results:

Among 6732 children, 68% were prescribed opioids (range = 1–65 d, median = 4 d, IQR = 3–5 d). Patients discharged by general surgery services were prescribed 1.23 (95% CI = 1.06–1.42) excess days of opioids, compared with those discharged by pediatric surgery services. Risk of ED visit for constipation (n = 61, 1%) was increased with opioid prescription [1–3 d, risk ratio (RR) = 2.46, 95% CI = 1.31–5.78; 4–6 d, RR = 1.89, 95% CI = 0.83–4.67; 7–14 d, RR = 3.75, 95% CI = 1.38–9.44; >14 d, RR = 6.27, 95% CI = 1.23–19.68], compared with no opioid prescription. There was similar or increased risk of ED visit for pain (n = 319, 5%) with opioid prescription [1–3 d, RR = 1.00, 95% confidence interval (CI) = 0.74–1.32; 4–6 d, RR = 1.31, 95% CI = 0.99–1.73; 7–14 d, RR = 1.52, 95% CI = 1.00–2.18], compared with no opioid prescription. Likewise, need for refill (n = 157, 3%) was not associated with initial days of opioid prescribed (reference 1–3 d; 4–6 d, RR = 0.96, 95% CI = 0.68–1.35; 7–14 d, RR = 0.91, 95% CI = 0.49–1.46; and >14 d, RR = 1.22, 95% CI = 0.59–2.07).

Conclusions:

There was substantial variation in opioid prescribing patterns. Opioid prescription duration increased risk of ED visits for constipation, but not for pain or refill.
NASA-Task Load Index Differentiates Surgical Approach
Authors: Law Katherine E. , Lowndes Bethany R. , Kelley Scott R. , Blocker Renaldo C. , Larson David W. , Hallbeck M. Susan , Nelson Heidi
Published: January 2019

Objective:

Surgeon workload, or human “cost” of performing a procedure, is not well understood in light of emerging surgical technologies. This pilot study quantified surgeon workload for colorectal procedures and identified patient, surgeon, and procedural factors impacting workload.

Summary Background Data:

Innovative technologies and procedures in surgery have generally been promoted for the advancement of patient care. The resulting surgeon workload is poorly studied with little knowledge of the contributing factors impacting workload.

Methods:

Surgeons completed NASA-Task Load Index (NASA-TLX) questionnaires to self-assess workload following abdominopelvic colon and rectal procedures. Corresponding patient data were retrieved from the medical record. Descriptive statistics, correlations, and ANOVA were performed to compare surgeon and patient factors, procedure type, and surgical approach on workload overall and by subscales.

Results:

Seven attending surgeons rated 238 surgeries, of which 218 (92%) had corresponding patient data. Surgeon experience and patient demographics had inconsistent effects on workload. A statistically significant 3-way interaction was identified among disease process, procedure type, and surgical approach on workload (F(9, 146) = 2.17, P = 0.027), but was limited to open procedures for neoplasia and inflammatory bowel disease patients. Proctectomy and colectomy procedures compared across open, laparoscopic, and robotic approaches showed significant differences in overall workload and subscales, where the robotic procedures required significantly less mental demand, physical demand, and effort, than open or laparoscopic (P < 0.05).

Conclusions:

Patient characteristics, disease process, and surgical experience had inconsistent effects on surgeon workload. Major differences in workload were identified for procedure type and surgical approach, where robotic procedures required less mental demand, physical demand, and effort.
The dynamics of granular flow from a silo with two symmetric openings
Authors: Fullard L. A. , Breard E. C. P. , Davies C. E. , Godfrey A. J. R. , Fukuoka M. , Wade A. , Dufek J. , Lube G.
Published: January 2019

The dynamics of granular flow in a rectangular silo with two symmetrically placed exit openings is investigated using particle image velocimetry (PIV), flow rate measurements and discrete element modelling (DEM). The flow of mustard seeds in a Perspex silo is recorded using a high-speed camera and the resulting image frames are analysed using PIV to obtain velocity, velocity divergence and shear rate plots. A change in flow structure is observed as the distanceLbetween the two openings is varied. The mass flow rate is shown to be at a maximum at zero opening separation, decreasing asLis increased; it then reaches a minimum before rising to an equilibrium rate close to two times that of an isolated (non-interacting) opening. The flow rate experiment is repeated using amaranth and screened sand and similar behaviour is observed. Although this result is in contrast with some recent DEM and physical experiments in silo systems, this effect has been reported in an analogous system: the evacuation of pedestrians from a room through two doors. Our experimental results are replicated using DEM and we show that inter-particle friction controls the flow rate behaviour and explains the discrepancies in the literature results.
Union bound for quantum information processing
Authors: Khabbazi Oskouei Samad , Mancini Stefano , Wilde Mark M.
Published: January 2019

In this paper, we prove a quantum union bound that is relevant when performing a sequence of binary-outcome quantum measurements on a quantum state. The quantum union bound proved here involves a tunable parameter that can be optimized, and this tunable parameter plays a similar role to a parameter involved in the Hayashi–Nagaoka inequality (Hayashi & Nagaoka 2003
IEEE Trans. Inf. Theory
49
, 1753–1768. (
doi:10.1109/TIT.2003.813556
)), used often in quantum information theory when analysing the error probability of a square-root measurement. An advantage of the proof delivered here is that it is elementary, relying only on basic properties of projectors, Pythagoras' theorem, and the Cauchy–Schwarz inequality. As a non-trivial application of our quantum union bound, we prove that a sequential decoding strategy for classical communication over a quantum channel achieves a lower bound on the channel's second-order coding rate. This demonstrates the advantage of our quantum union bound in the non-asymptotic regime, in which a communication channel is called a finite number of times. We expect that the bound will find a range of applications in quantum communication theory, quantum algorithms and quantum complexity theory.
Horizontally isotropic double porosity convection
Authors: Straughan B.
Published: January 2019

We analyse instability and nonlinear stability in a layer of saturated double porosity medium. In a double porosity or bidisperse porous medium, there are normal pores which give rise to a macroporosity. But, there are also cracks or fissures in the solid skeleton and these give arise to another porosity known as micro porosity. In this paper, the macropermeability is horizontally isotropic, in the sense that the vertical component of permeability is different to the horizontal one which is the same in all horizontal directions. Thus, the permeability is transversely isotropic with the isotropy axis in the vertical direction of gravity. We also allow the micro permeability to be horizontally isotropic, but the permeability ratios of vertical to horizontal are different in the macro- and micro-phases. The effect of the difference of ratios is examined in detail.
Trade-offs direct the evolution of coloration in Galápagos land snails
Authors: Kraemer A. C. , Philip C. W. , Rankin A. M. , Parent C. E.
Published: January 2019

Increasingly, multiple selective factors are recognized as jointly contributing to the evolution of morphology. What is not clear is how these forces vary across communities to promote morphological diversification among related species. In this study of Galápagos endemic snails (genusNaesiotus), we test several hypotheses of colour evolution. We observe mockingbirds (genusMimus) predating live snails and find that avian predation selects against conspicuous shells. The evolutionary outcome of this selection is a diversity of shell colours across snails of the archipelago, each closely matching local backgrounds. We also find that snails more regularly exposed to the hot, equatorial sun reflect more light than shells of species from shadier habitats, suggesting a role for thermoregulatory constraints directing colour evolution. The signature of thermoregulatory selection is most clear in comparatively young communities (on the youngest islands), while the signature of selection from predators is most evident in older communities (on the older islands). Together, our findings point to a scenario of shifting selective forces along island ontogeny and community maturity that lead to the distribution of snail coloration we observe in Galápagos. Complex selective regimes such as these may have more responsibility for morphological diversity than is currently recognized.
New Caledonian crows infer the weight of objects from observing their movements in a breeze
Authors: Jelbert Sarah A. , Miller Rachael , Schiestl Martina , Boeckle Markus , Cheke Lucy G. , Gray Russell D. , Taylor Alex H. , Clayton Nicola S.
Published: January 2019

Humans use a variety of cues to infer an object's weight, including how easily objects can be moved. For example, if we observe an object being blown down the street by the wind, we can infer that it is light. Here, we tested whether New Caledonian crows make this type of inference. After training that only one type of object (either light or heavy) was rewarded when dropped into a food dispenser, birds observed pairs of novel objects (one light and one heavy) suspended from strings in front of an electric fan. The fan was either on—creating a breeze which buffeted the light, but not the heavy, object—or off, leaving both objects stationary. In subsequent test trials, birds could drop one, or both, of the novel objects into the food dispenser. Despite having no opportunity to handle these objects prior to testing, birds touched the correct object (light or heavy) first in 73% of experimental trials, and were at chance in control trials. Our results suggest that birds used pre-existing knowledge about the behaviour exhibited by differently weighted objects in the wind to infer their weight, using this information to guide their choices.
Imperfect vaccine and hysteresis
Authors: Chen Xingru , Fu Feng
Published: January 2019

Addressing vaccine compliance problems is of particular relevance and significance to public health. Despite resurgence of vaccine-preventable diseases and public awareness of vaccine importance, why is it so challenging to boost population vaccination coverage to desired levels especially in the wake of declining vaccine uptake? To understand this puzzling phenomenon, here we study how social imitation dynamics of vaccination can be impacted by the presence of imperfect vaccine, which only confers partial protection against the disease. Besides weighing the perceived cost of vaccination with the risk of infection, the effectiveness of vaccination is also an important factor driving vaccination decisions. We discover that there can exist multiple stable vaccination equilibria if vaccine efficacy is below a certain threshold. Furthermore, our bifurcation analysis reveals the occurrence of
hysteresis loops
of vaccination rate with respect to changes in the perceived vaccination cost as well as in the vaccination effectiveness. Moreover, we find that hysteresis is more likely to arise in spatial populations than in well-mixed populations, even for parameter choices that do not allow for bifurcation in the latter. Our work shows that hysteresis can appear as an unprecedented roadblock for the recovery of vaccination uptake, thereby helping explain the persistence of vaccine compliance problem.
Missense variants in health and disease affect distinct functional pathways and proteomics features
Authors: Laddach Anna , Ng Joseph Chi-Fung , Fraternali Franca
Published: January 2019

1

Missense variants are present amongst the healthy population, but some of them are causative of human diseases. Therefore, a classification of variants associated with “healthy” or “diseased” states is not always straightforward. A deeper understanding of the nature of missense variants in health and disease, the cellular processes they may affect, and the general molecular principles which underlie these differences, is essential to better distinguish pathogenic from population variants. Here we quantify variant enrichment across full-length proteins, their domains and 3D-structure defined regions. We integrate this with available transcriptomic and proteomic (protein half-life, thermal stability, abundance) data. Using this approach we have mined a rich set of molecular features which enable us to understand the differences underlying pathogenic and population variants: pathogenic variants mainly affect proteins involved in cell proliferation and nucleotide processing, localise to protein cores and interaction interfaces, and are enriched in more abundant proteins. In terms of their molecular properties, we find that common population variants and pathogenic variants show the greatest contrast. Additionally, in contrary to other studies, we find that rare population variants display features closer to common than pathogenic variants. This study provides molecular details into how different proteins exhibit resilience and/or sensitivity towards missense variants. Such details could be harnessed to predict variant deleteriousness, and prioritise variant-enriched proteins and protein domains for therapeutic targeting and development. The ZoomVar database, which we created for this study, is available at http://fraternalilab.kcl.ac.uk/ZoomVar. It allows users to programmatically annotate a large number of missense variants with protein structural information, and to calculate variant enrichment in different protein structural regions.

Significance Statement

One of the greatest challenges in understanding the genetic basis of diseases is to discriminate between likely harmless and potentially disease-causing sequence variants. To better evaluate the pathogenic potential of missense variants, we developed a strategy to quantitatively measure the enrichment of both disease and non disease-related variants within a protein based on its structural and domain organisation. By integrating available transcriptomics and proteomics data, our approach distinguishes pathogenic from population variants far more clearly than previously possible, and reveals hitherto unknown details of how different proteins exhibit resilience and/or sensitivity towards genetic variants. Our results will help to prioritise variant-enriched proteins for therapeutic targeting; we have created the ZoomVar database, accessible at http://fraternalilab.kcl.ac.uk/ZoomVar, for programmatic mapping of user-defined variants to protein structural and domain information.
3’-5’ crosstalk contributes to transcriptional bursting
Authors: Cavallaro Massimo , Walsh Mark D. , Jones Matt , Teahan James , Tiberi Simone , Finkenstädt Bärbel , Hebenstreit Daniel
Published: January 2019

Background

Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3’ and 5’ ends of a gene that enable reinitiation of transcription upon termination.

Results

Using Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment.

Conclusions

Interactions between the 3’ and 5’ ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.
Intra-lineage Plasticity and Functional Reprogramming Maintain Natural Killer Cell Repertoire Diversity
Authors: Pfefferle Aline , Jacobs Benedikt , Ask Eivind Heggernes , Lorenz Susanne , Clancy Trevor , Goodridge Jodie P. , Sohlberg Ebba , Malmberg Karl-Johan
Published: January 2019

Natural killer (NK) cell repertoires are made up of a vast number of phenotypically distinct subsets with different functional properties. The molecular programs involved in maintaining NK cell repertoire diversity under homeostatic conditions remains elusive. Here we show that subset-specific NK cell proliferation kinetics correlate with mTOR activation, and that global repertoire diversity is maintained through a high degree of intra-lineage subset plasticity during IL-15-driven homeostatic proliferation in vitro. High-resolution flow cytometry and single cell RNA sequencing revealed that slowly cycling sorted KIR+CD56dim NK cells with an induced CD57 phenotype display increased functional potential associated with inhibitory MHC interactions and activating DAP12 signaling. In contrast, rapidly cycling cells upregulate NKG2A and display a general loss of functionality associated with a transcriptional increase in RNA-binding metabolic enzymes and cytokine signaling pathways. These results shed new light on the role of intra-lineage plasticity during NK cell homeostasis and suggest that the functional fate of the cell is tightly linked to the acquired phenotype and determined by transcriptional reprogramming.

One Sentence Summary:

High-resolution flow cytometry combined with single-cell RNA sequencing reveal a role for intra-lineage plasticity and functional reprogramming in maintaining phenotypically and functionally diverse NK cell repertoires during IL-15-driven homeostatic proliferation.
egKnock: identifying direct gene knockout strategies for microbial strain optimization based on metabolic network with gene-protein-reaction relationships
Authors: Xu Zixiang
Published: January 2019

Background

Gene knockout method has been used to improve the conversion ratio of industrial strains for many chemical products. There are a series of published algorithms to predict the targets for deletion. Based on metabolic networks, many of these algorithms are designed to predict the target of reaction or enzyme deletion. But as for the many-to-many relationship between genes and reactions, reaction or enzyme deletion is not the ideal strategy for metabolic engineering. GDLS algorithm aims to find direct gene deletion target by using local search, but it actually ignores the logic relationship of gene-protein-reaction.

Results

In this study, we aim to find direct gene deletion targets for metabolic network, but the logic relationship of gene-protein-reaction (GPR) is considered. Our algorithm is call egKnock. At the same time, egKnock will provide the solution with multiple strategies and can maximize the minimum target flux of industrial objective in flux variability analysis. We compare egKnock with the algorithm of GDLS and OptORF by predicting the targets of gene deletion for several chemical products with their flux balance analysis testification, flux variability analysis testification and the main flux distribution.

Conclusions

By comparison with the algorithm of GDLS and OptORF, we can conclude that egKnock is a nice algorithm for identifying direct gene knockout strategies for microbial strain optimization.
Visual Entrainment at 10 Hz causes periodic modulation of the Flash Lag Illusion
Authors: Chota Samson , VanRullen Rufin
Published: January 2019

It has long been debated whether visual processing is, at least partially, a discrete process. Although vision appears to be a continuous stream of sensory information, sophisticated experiments reveal periodic modulations of perception and behavior. Previous work has demonstrated that the phase of endogenous neural oscillations in the 10 Hz range predicts the “lag” of the flash lag effect, a temporal visual illusion in which a static object is perceived to be lagging in time behind a moving object. Consequently, it has been proposed that the flash lag illusion could be a manifestation of a periodic, discrete sampling mechanism in the visual system. In this experiment we set out to causally test this hypothesis by entraining the visual system to a periodic 10 Hz stimulus and probing the flash lag effect (FLE) at different time points during entrainment. We hypothesized that the perceived FLE would be modulated over time, at the same frequency as the entrainer (10 Hz). A frequency analysis of the average FLE time-course indeed reveals a significant peak at 10 Hz as well as a strong phase consistency between subjects (N=26). Our findings provide evidence for a causal relationship between alpha oscillations and fluctuations in temporal perception.
Light-mediated circuit switching in the Drosophila neuronal clock network
Authors: Schlichting M , Weidner P , Diaz M , Menegazzi P , Dalla-Benetta E , Helfrich-Förster C , Rosbash M
Published: January 2019

The circadian clock is a timekeeper but also helps adapt physiology to the outside world. This is because an essential feature of clocks is their ability to adjust (entrain) to the environment, with light being the most important signal. Whereas Cryptochrome-mediated entrainment is well understood in Drosophila, integration of light information via the visual system lacks a neuronal or molecular mechanism. Here we show that a single photoreceptor sub-type is essential for long day adaptation. These cells activate key circadian neurons, namely the lLNvs, which release the neuropeptide PDF. Using a cell-specific CRISPR/Cas9 assay, we show that PDF directly interacts with neurons important for evening (E) activity timing. Interestingly, this pathway is specific for light entrainment and appears to be dispensable in constant darkness (DD). The results therefore indicate that external cues cause a rearrangement of neuronal hierarchy, which is a novel form of plasticity.
Trace metal availability affects greenhouse gas emissions and microbial functional group abundance in freshwater wetland sediments
Authors: Giannopoulos Georgios , Hartop Katherine R. , Brown Bonnie L. , Franklin Rima B.
Published: January 2019

We investigated the effects of trace metal additions on microbial nitrogen and carbon cycling using freshwater wetland sediment microcosms amended with μM concentrations of copper (Cu), molybdenum (Mo), iron (Fe), and all combinations. In addition to monitoring inorganic nitrogen transformations (NO3−, NO2−, N2O, NH4+) and carbon mineralization (CO2, CH4), we tracked changes in functional gene abundance associated with denitrification (nirS,nirK,nosZ), DNRA (nrfA), and methanogenesis (mcrA). Greater availability of Cu led to more complete denitrification (i.e., less N2O accumulation) and a higher abundance of thenirKandnosZgenes, which encode for Cu-dependent reductases. We found sparse evidence of DNRA activity and no consistent effect on CO2production. Contrary, net CH4production was stimulated by the trace metal amendments and the Mo additions, in particular, led to increasedmcrAgene abundance. Taken together, these findings demonstrate that trace metal effects on microbial physiology, which have heretofore only been studied in pure culture, can impact community-level function. We observed direct and indirect effects on both nitrogen and carbon biogeochemistry that culminated in increased production of greenhouse gasses, and the shifts in functional group abundance that we documented suggest these responses may have been mediated through changes in microbial community composition. Overall, this work supports a more holistic consideration of metal effects on environmental microbial communities that recognizes the key role that metal limitation plays in microbial physiology.