bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of Neurotized Hypothenar Free Perforator Flaps Used for Fingertip Reconstruction
Authors: Dağdelen Dağhan , Aksoy Alper
Published: September 2019

Introduction

In reconstruction of digital amputations of the upper extremity, composite tissue alternatives with similar features are limited for finger tip reconstruction. Among these alternatives, free perforator flaps elevated from the hypothenar region (HFPFs) are defined, but reluctancy goes on for utilization of these flaps.

In this study, we aimed to highlight the sensory results of HFPFs when a neural repair is incorporated to the flap and also to justify their usage by presenting functional and aesthetic outcomes of the reconstructions performed with HFPFs.

Methods

This clinical study was conducted from June 2015 to June 2017. Twelve patients with acute finger tip amputations were examined. Distal amputation levels were subgrouped according to Ishikawa classification. Patient demographics and amputation etiology were listed. All fingertip defects were reconstructed with a neurotized HFPF. All perforator anastomoses were performed in an end-to-end fashion. During follow-up, 2-point discrimination and dynamometric test were conducted. In addition, the Michigan Hand Outcomes Questionnaire was carried out. Evaluation of the results from a cosmetic standpoint was also conducted, with 4 blinded, independent surgeons using the visual analog scale.

Results

Of 12 digital amputations reconstructed with neurotized HFPFs, 10 were totally viable during follow-up, whereas partial loss was observed in 2 flaps. The mean age was 38.8 ± 11.8 years. Most of the amputations were classified as Ishikawa subgroup 2 (50%). The mean dynamic 2-point discrimination was 3.2 ± 0.11 mm and slightly greater compared with contralateral digit (P = 0.003). Also minor decreases were measured in forced grip and pulp-to-pulp grip strengths (P = 0.003). Overall satisfaction was 92.7% in Michigan Hand Outcomes Questionnaire. Average visual analog scale score was 7.25 out of 10.

Conclusions

Hypothenar free perforator flaps, with incorporation of neural repair, give promising results for reconstruction of the fingertip. In addition to superior sensorial outcomes, HFPFs yield satisfying results from aesthetic and functional perspectives.
Advancements in Reconstructive Surgery Broaden Opportunities for Salvage of the Injured Lower Extremity
Authors: Assi Patrick E. , Giladi Aviram M.
Published: September 2019

Advancements in microsurgery have made lower extremity reconstruction possible even after major soft tissue loss or tibial nerve disruption. There is an ongoing paradigm shift in the indications for amputation versus salvage and in flap selection protocols for different areas of the lower extremity. Initial evaluation, patient selection, triage, and timing of reconstruction are essential factors that can influence functional and aesthetic outcomes. The emergence of perforator flaps and the application of new concepts such as free-style flaps, propeller perforator flaps, thinning of free flaps, and supermicrosurgery have provided reconstructive surgeons with many techniques to decrease donor-site morbidity and improve outcomes. This includes options for reconstruction on extremities with single or no adequate runoff vessels. We present a review of the major advancements in reconstructive surgery for salvage of the traumatic lower extremity.
Clinical Application of Precise Composite Breast Augmentation
Authors: Shi Yanyan , Sun Haiyang , Fang Jun , Yang Zhenyu , Jiang Ping , Tan Xiaoyan
Published: September 2019

Objective

For thin women with little subcutaneous fat and micromastia, they could not obtain ideal results by choosing autologous fat breast augmentation or prosthesis-only breast augmentation. To address these problems, we combined autologous fat and prosthesis for breast augmentation, and the clinical results were satisfactory.

Methods

Eleven cases of composite breast augmentation from 2014 to 2017 were analyzed retrospectively. Postoperative follow-up and evaluation were completed. The operations were performed through a subaxillary incision, and the round, high-convex breast prostheses were implanted into the retropectoralis major space. Autologous fat was injected into subcutaneous, retromammary, and prepectoralis layers to cover the whole breast before and after implanting the prosthesis.

Results

The mean follow-up period was 16 months (range, 6–36 months). All patients were satisfied with the size of their breasts. Postoperative complications such as infection, vascular embolism, delayed healing incision, hematoma, and seroma were not detected. In 1 case, the sensation of a unilateral nipple-areola was decreased initially but recovered after 4 months. Long-term complications such as capsular contracture, palpable nodules, double-bubble deformity, asymmetry, poor handling, implant edge visibility, and palpability also did not occur.

Conclusion

Breast augmentation combining autologous fat and prosthesis was safe and could achieve aesthetically satisfactory results.
Dermatologic Biopsy of Silicone Nasal Implant and Revision Rhinoplasty in the Asian Patient, A Cautionary Report
Authors: Khan Saiqa , Kotick James , Khasawneh Raed , Lim Alan
Published: September 2019

Care provided to the Asian rhinoplasty patient may be multidisciplinary at times, including not only plastic surgeons, but also other health care professionals. It is crucial that all physicians caring for these patients practice complete awareness of the patient's prior operations and details of materials used in order to optimize results and avoid potentially devastating complications. These complications include but are not limited to implant infection and extrusion. Here the authors describe one such case report, discussing dermatologic biopsy of a silicone implant of the nasal tip and dorsum and subsequent revision rhinoplasty with implant removal and costochondral graft placement.
Combined Use of Specially-Designed Digital Surgical Guides and Pre-Formed Reconstruction Plate to Treat Bilateral Mandibular Fracture
Authors: Huang Yanling , Xia Zhuoyu , Zhang Xiaojie , Liao Xuejuan , Guo Zeyou , Ji Suhui , Long Jie
Published: September 2019

This paper describes the application of a modified digital surgical guide, an occlusal template and a pre-formed reconstruction titanium plate in the open reduction and internal fixation of a bilateral mandibular fracture. Bilateral mandibular fracture is a commonly encountered simple type of fracture. However, even for an experience surgeon, achieving precise treatment remains a challenge due to the movable temporomandibular joint, unstable fractured segments, the difficulty in forming a reconstruction plate, and the lack of an effective stabilizing and locating device. In this case, the surgeon used a specially-designed modified guide together with a reconstruction plate and an occlusal template to treat a bilateral mandible fracture, effectively improving the accuracy and the medical outcome of the operation, saving operation time and reducing postoperative complications.
Expanding a Foot Care Education Program for Nurses
Authors: Beuscher Tara L. , Moe Hollie L. , Stolder Mary Ellen , Peloquin Lois , Nesbitt Bonnie
Published: September 2019

Faculty of a foot care continuing education program in the Midwest sought to determine current practice and interest in expanding the current program, both didactic and clinical, to meet expanded requirements in certification criteria. An electronic e-mail survey with both quantitative and qualitative questions was developed and sent to 445 past participants who completed the Foot and Nail Care: Education for Nurses Program hosted by the University of Wisconsin–Eau Claire Continuing Education over the past 5 years. There were 99 responses for a response rate of 22%. We asked several questions about clinical practice specific to the use of equipment, roles and responsibilities, and practice sites. Most participants used a mechanical rotary file for debriding toenails in their practices, with almost half having obtained a more advanced rotary file the longer they practiced. Most participants practiced in a variety of roles and settings including part of their paid employment, an independent business (full- or part-time), or volunteer. Less than half of respondents have become certified in the specialty. Those who have sought certification have chosen either the Wound Ostomy Continence Nursing Certification Board's Certified Foot Care Nurse or the American Foot Care Nurses Association's Certified Foot Care Specialist (CFCS). Sufficient interest (77%; n = 75) was expressed to expand the course to meet the requirements of certification, specifically for clinical hours. Based on the results of this survey, we concluded there is value in offering the program with several modules where participants could complete an introductory course and have the option to participate in continued education should they decide to learn more, seek certification, or need continuing education for recertification.
Brice Bosnich. 3 June 1936—13 April 2015
Authors: Bennett Martin A.
Published: September 2019

Brice Bosnich, an Australian inorganic chemist, graduated from the University of Sydney and obtained his PhD at the Australian National University, Canberra. He then worked successively at University College London, the University of Toronto and the University of Chicago. He had an abiding interest in stereochemistry and its relationship with chemical reactivity, and in the chirality and optical activity of coordination and organometallic complexes, mainly those of the d-block elements. His early studies concerned the topological and conformational behaviour of classical coordination compounds, mainly of cobalt(III), and made extensive use of the technique of circular dichroism. He put this background to elegant use in perhaps his most distinctive work, namely, the design and synthesis of a
C
2
-symmetric ditertiary phosphine, (
S
,
S
)-chiraphos, the rhodium(I) complex [Rh{Ph
2
PCH(CH
3
)CH(CH
3
)PPh
2
}]
+
of which catalysed efficiently the homogeneous hydrogenation of prochiral enamides to amino acids in high optical purity. Bosnich traced the high enantioselectivity to the chiral array of P-phenyl substituents that is generated on coordination of (
S
,
S
)-chiraphos. In principle, catalytic enantioselective synthesis represents a powerful and economic method of introducing chirality into the synthesis of biologically active molecules, which, since the thalidomide tragedy, are required to be marketed only in optically pure forms. Dissymmetric ligands similar to (
S
,
S
)-chiraphos are now routinely employed in this type of synthesis. Bosnich developed several other enantioselective processes based on organo-transition metal chemistry. He also had several quasi-theoretical interests, including the possible use of circular dichroism to determine the absolute configuration of chiral metal complexes, and the development of a molecular mechanics force field for metallocenes. He maintained a strong interest in the properties of multimetallic proteins and devoted much effort to the construction of chiral binucleating ligands. During the 7–8 years before his retirement from the University of Chicago in 2006, he shifted his research to supramolecular recognition by suitably designed metal complexes.
The effect of social preference on academic diligence in adolescence
Authors: Andrews J. L. , Foulkes L. , Griffin C. , Blakemore S. J.
Published: September 2019

In the current study, we were interested in whether adolescents show a preference for social stimuli compared with non-social stimuli in the context of academic diligence, that is, the ability to expend effort on tedious tasks that have long-term benefits. Forty-five female adolescents (aged 11–17) and 46 female adults (aged 23–33) carried out an adapted version of the Academic Diligence Task (ADT). We created two variations of the ADT: a social ADT and non-social ADT. Individuals were required to freely split their time between an easy, boring arithmetic task and looking at a show-reel of photographs of people (in the social ADT) or landscapes (in the non-social ADT). Individuals also provided enjoyment ratings for both the arithmetic task and the set of photographs they viewed. Adolescents reported enjoying the social photographs significantly more than the non-social photographs, with the converse being true for adults. There was no significant difference in the time spent looking at the social photographs between the adolescents and adults. However, adults spent significantly more time than adolescents looking at the non-social photographs, suggesting that adolescents were less motivated to look at the non-social stimuli. Further, the correlation between self-reported enjoyment of the pictures and choice behaviour in the ADT was stronger for adults than for adolescents in the non-social condition, revealing a greater discrepancy between self-reported enjoyment and ADT choice behaviour for adolescents. Our results are discussed within the context of the development of social cognition and introspective awareness between adolescence and adulthood.
Characterization of bioadsorbent produced using incorporated treatment of chemical and carbonization procedures
Authors: Lee Chuan Li , H'ng Paik San , Chin Kit Ling , Paridah Md Tahir , Rashid Umer , Go Wen Ze
Published: September 2019

The production of bioadsorbent from palm kernel shell (PKS) and coconut shell (CS) pretreated with 30% phosphoric acid (H
3
PO
4
) was optimized using the response surface methodology (RSM). Iodine adsorption for both bioadsorbents was optimized by central composite design. Two parameters including the H
3
PO
4
pretreatment temperature and carbonization temperature were determined as significant factors to improve the iodine adsorption of the bioadsorbent. Statistical analysis results divulge that both factors had significant effect on the iodine adsorption for the bioadsorbent. From the RSM analysis, it was suggested that using 80 and 79°C as H
3
PO
4
pretreatment temperature and 714 and 715°C as carbonization temperature would enhance the iodine adsorption of the CS and PKS bioadsobent, respectively. These results indicated that H
3
PO
4
is a good pretreatment for preparing PKS and CS prior to carbonization process to produce bioadsorbent with well-developed microporous and mesoporous volume. The effort to produce alternative high grade and inexpensive adsorbent derived from lignocellulosic biomass, particularly in the nut shell form was implied in this research.
Foraging ecology of African wolves (
Canis lupaster
) and its implications for the conservation of Ethiopian wolves (
Canis simensis
)
Authors: Gutema Tariku Mekonnen , Atickem Anagaw , Tsegaye Diress , Bekele Afework , Sillero-Zubiri Claudio , Marino Jorgelina , Kasso Mohammed , Venkataraman Vivek V. , Fashing Peter J. , Stenseth Nils C.
Published: September 2019

African wolves (AWs) are sympatric with endangered Ethiopian wolves (EWs) in parts of their range. Scat analyses have suggested a dietary overlap between AWs and EWs, raising the potential for exploitative competition, and a possible conservation threat to EWs. However, in contrast to that of the well-studied EW, the foraging ecology of AWs remains poorly characterized. Accordingly, we studied the foraging ecology of radio-collared AWs (
n
= 11 individuals) at two localities with varying levels of anthropogenic disturbance in the Ethiopian Highlands, the Guassa-Menz Community Conservation Area (GMCCA) and Borena-Saynt National Park (BSNP), accumulating 845 h of focal observation across 2952 feeding events. We also monitored rodent abundance and rodent trapping activity by local farmers who experience conflict with AWs. The AW diet consisted largely of rodents (22.0%), insects (24.8%), and goats and sheep (24.3%). Of the total rodents captured by farmers using local traps during peak barley production (July to November) in GMCCA, averaging 24.7 ± 8.5 rodents/hectare/day, 81% (
N
= 3009) were scavenged by AWs. Further, of all the rodents consumed by AWs, most (74%) were carcasses. These results reveal complex interactions between AWs and local farmers, and highlight the scavenging niche occupied by AWs in anthropogenically altered landscapes in contrast to the active hunting exhibited by EWs in more intact habitats. While AWs cause economic damage to local farmers through livestock predation, they appear to play an important role in scavenging pest rodents among farmlands, a pattern of behaviour which likely mitigates direct and indirect competition with EWs. We suggest two routes to promote the coexistence of AWs and EWs in the Ethiopian highlands: local education efforts highlighting the complex role AWs play in highland ecosystems to reduce their persecution, and enforced protection of intact habitats to preserve habitat preferred by EWs.
Effects of seepage and weak interlayer on the failure modes of surrounding rock: model tests and numerical analysis
Authors: Hu Jing , Wen Haijia , Xie Qilong , Li Binyang , Mo Qu
Published: September 2019

The presence of weak interlayers and groundwater are common adverse geological conditions in tunnels. To investigate the modes of failure of rock masses surrounding tunnels owing to weak interlayers and groundwater, model tests and numerical simulations were conducted in this study based on two cases, and a model that considers only the weak interlayer was conducted for comparison. Based on the tests, differences between two models in terms of rock pressure, displacement, cracks and strain were analysed. The results reveal that the presence of groundwater has a significant effect on the space–time distribution of stress, displacement and cracks in the surrounding rock. Furthermore, based on the numerical model, the seepage field was analysed in terms of pore water pressure, permeability and the seepage process to understand the joint action of groundwater and weak interlayer on the failure mechanism of tunnels. The results show that the groundwater and interlayer complement each other to induce the failure mode of the surrounding rock. The water accelerates slip in the interlayer and the development of cracks. Conversely, low strength, muddy weak interlayers serve as the channels of water flow, resulting in deformations and cracks at different locations and different failure modes.
How long do anti-predator interventions remain effective? Patterns, thresholds and uncertainty
Authors: Khorozyan Igor , Waltert Matthias
Published: September 2019

Human–predator conflicts are globally widespread, and effective interventions are essential to protect human assets from predator attacks. As effectiveness also has a temporal dimension, it is of importance to know how long interventions remain most effective and to determine time thresholds at which effectiveness begins to decrease. To address this, we conducted a systematic review of the temporal changes in the effectiveness of non-invasive interventions against terrestrial mammalian predators, defining a temporal trend line of effectiveness for each published case. We found only 26 cases from 14 publications, mainly referring to electric fences (
n
= 7 cases) and deterrents (
n
= 7 cases). We found electric fences and calving control to remain highly effective for the longest time, reducing damage by 100% for periods between three months and 3 years. The effectiveness of acoustical and light deterrents as well as guarding animals eroded quite fast after one to five months. Supplemental feeding was found to be counter-productive by increasing damage over time instead of reducing it. We stress that it is vital to make monitoring a routine requirement for all intervention applications and suggest to standardize periods of time over which monitoring can produce meaningful and affordable information.
Carbon dots functionalized papers for high-throughput sensing of 4-chloroethcathinone and its analogues in crime sites
Authors: Yen Yao-Te , Lin Yu-Syuan , Chen Ting-Yueh , Chyueh San-Chong , Chang Huan-Tsung
Published: September 2019

Sensitive and selective assays are demanded for quantitation of new psychoactive substances such as 4-chloroethcathinone that is a π-conjugated keto compound. Carbon dots (C-dots) prepared from L-arginine through a hydrothermal route have been used for quantitation of 4-chloroethcathinone in aqueous solution and on C-dot-functionalized papers (CDFPs). To prepare CDFPs, chromatography papers, each with a pattern of 8 × 12 circles (wells), are first fabricated through a solid-ink printing method and then the C-dots are coated into the wells. π-Conjugated keto or ester compounds induce photoluminescence quenching of C-dots through an electron transfer process. At pH 7.0, the CDFPs allow screening of abused drugs such as cocaine, heroin and cathinones. Because of poor solubility of heroin and cocaine at pH 11.0, the C-dot probe is selective for cathinones. The C-dots in aqueous solution and CDFPs at pH 11.0 allow quantitation of 4-chloroethcathinone down to 1.73 mM and 0.14 mM, respectively. Our sensing system consisting of a portable UV-lamp, a smartphone and a low-cost CDFP has been used to detect cathinones, cocaine and heroin at pH 7.0, showing its potential for screening of these drugs in crime sites.
Quality analysis of Makgeolli made with non-steamed rice flour Nuruk by various fungal strains
Authors: Lee Cheol-Gyo , Na Ji-Hoon , Park Sang-Jun , Jeong Jae-Hee , Kim Cheol-Min , Kim Bok-seon , Han Hong-Bi , Huh Chang-Ki
Published: September 2019

An easy and simple method of producing Nuruk using rice was developed. In addition, the quality characteristics of the prepared Nuruk were evaluated for Makgeolli production. A comparison of the enzyme activities between A. kawachii rice Koji (RK) and non-steamed rice flour Nuruk according to the fungal strain revealed the β-amylase activity of A. oryzae rice flour Nuruk (AON) to be the highest at 3697.85 SP/g. The α-amylase activity and protease activity were highest at 111.67 A.U and 33.23 tyrosine mg/min of P. candidum rice flour Nuruk (PCN), respectively. The ethanol contents of the four samples were similar at 16.1-16.4%. The sensory evaluation result showed that Makgeolli made with PCN had the highest preference score of 5.78 and showed a significant difference in overall preference. Moreover, Makgeolli made with PCN showed a higher preference than of Makgeolli made with RK. The titratable acidity and reducing sugar content of Makgeolli made with PCN were 0.48% and 4.14%, respectively, which were higher than those of Makgeolli made with RK. The ethanol content of Makgeolli made with PCN was 15.10%, which showed a 12.80% higher ethanol production yield than that of Makgeolli made with RK. Therefore the PCN produced in this study will be effective for Makgeolli production.
Quality characteristics and antioxidant activities of aged black Liriope platyphylla
Authors: Kim Da Hee , Oh Da Rae , Baek Seung Yeon , Kim Mee Ree
Published: September 2019

The purpose of this study was to examine the physicochemical properties and antioxidant activities of aged black Liriope platyphylla (ALP) and raw Liriope platyphylla (RLP). RLP was aged for 14 days at high humidity (90% and 95%) and temperatures (50℃ and 80℃). With the passage of the storage period, the moisture content significantly decreased to 64.26%. During storage, the sugar content increased to 16.00 °Brix, while the reducing sugar content increased to 2.62%. With increasing storage time, the pH decreased to 3.63, while the acidity increased to 0.032%. In the Hunter color system, L (lightness) and b (yellowness) values of ALP were lower than those of RLP, while the redness value of ALP was higher than that of RLP. During storage, the browning index value significantly increased to 77.08. The increase in total phenol content of ALP after 14 days of aging was more than that of RLP. IC50 values for both 1,1-diphenyl-2-picrylhydrazyl (DPPH) and hydroxyl radical scavenging activities of ALP after 14 days of aging were lower than those of RLP. Based on these results, it is suggested that aged black Liriope platyphyllas can a useful food material, in terms of both physicochemical properties and antioxidant activities.
A deep learning approach with event-related spectral EEG data in attentional deficit hyperactivity disorder
Authors: Dubreuil-Vall Laura , Ruffini Giulio , Camprodon Joan A.
Published: September 2019

Attention deficit hyperactivity disorder (ADHD) is a heterogeneous neurodevelopmental disorder that affects 5% of the pediatric and adult population worldwide. The diagnosis remains essentially clinical, based on history and exam, with no available biomarkers. In this paper, we describe a deep convolutional neural network (DCNN) for ADHD classification derived from the time-frequency decomposition of electroencephalography data (EEG), particularly of event-related potentials (ERP) during the Flanker Task collected from 20 ADHD adult patients and 20 healthy controls (HC). The model reaches a classification accuracy of 88%, superior to resting state EEG spectrograms and with the key advantage, compared with other machine learning approaches, of avoiding the need for manual selection of EEG spectral or channel features. Finally, through the use of feature visualization techniques, we show that the main features exciting the DCNN nodes are a decreased power in the alpha band and an increased power in the delta-theta band around 100ms for ADHD patients compared to HC, suggestive of attentional and inhibition deficits, which have been previously suggested as pathophyisiological signatures of ADHD. While confirmation with larger clinical samples is necessary, these results highlight the potential of this methodology to develop CNS biomarkers of practical clinical utility.
Mixed-stock analyses among migratory, non-native Chinook salmon at-sea and assignment to natal sites in freshwater at their introduced range in South America
Authors: Musleh Selim S. , Seeb Lisa W. , Seeb James E. , Ernst Billy , Neira Sergio , Harrod Chris , Gomez-Uchida Daniel
Published: September 2019

Invasive species with migratory behavior and complex life cycle represent a challenge for evaluating natal sites among individuals. Private and government-sponsored initiatives resulted in the successful introduction and naturalization of Chinook salmon (Oncorhynchus tshawytscha) throughout northern and southern Patagonia in South America. These migratory fish breed in freshwater, but spend most of their life at sea feeding, forming abundant populations in several watersheds draining into the southeast Pacific Ocean. We used single nucleotide polymorphisms (SNPs) combined with genetic structure and mixed-stock analyses to evaluate natal sites of Chinook salmon at-sea caught in one estuary and two coastal locations compared to reference populations from breeding sites in freshwater. Firstly, Bayesian individual-assignment analyses revealed no genetic structure among adults caught off the coast of the Toltén River and migrating (maturing) adults caught in Toltén River estuary, suggesting they likely belong to a single population. Secondly, mixed-stock genetic analyses revealed that most at-sea Chinook salmon caught in one estuary and two coastal locations likely originated from spawners from the nearest river (90-95%), with a small contribution from adjacent watersheds (5-10%). This appears consistent with Chinook salmon populations in their native range in which juveniles migrate short distances (100-200 km) from their river of origin to coastal feeding grounds, some of which became donor of propagules for non-native Chinook salmon populations under study. Mixed-stock genetic analyses provide considerable potential to identify the population of origin of Chinook salmon mixtures caught off the coast. They also seem an appropriate proof of concept to help identify potential immigrants from other watersheds as well as migration patterns and invasion pathways in a non-native species.
An Aryl Hydrocarbon Receptor from the CaecilianGymnopis multiplicataSuggests Low Dioxin Affinity in the Ancestor of All Three Amphibian Orders
Authors: Kazzaz Sarah A. , Tagliabue Sara Giani , Franks Diana G. , Denison Michael S. , Hahn Mark E. , Bonati Laura , Powell Wade H.
Published: September 2019

The aryl hydrocarbon receptor (AHR) plays pleiotropic roles in the development and physiology of vertebrates in conjunction with xenobiotic and endogenous ligands. It is best known for mediating the toxic effects of dioxin-like pollutants such as 2,3,7,8-tetracholordibenzo-p-dioxin (TCDD). While most vertebrates possess at least one AHR that binds TCDD tightly, amphibian AHRs bind TCDD with very low affinity. Previous analyses of AHRs fromXenopus laevis(a frog; order Anura) andAmbystoma mexicanum(a salamander; order Urodela) identified three amino acid residues in the ligand-binding domain (LBD) that underlie low-affinity binding. InX. laevisAHR1β, these are A354, A370, and N325. Here we extend the analysis of amphibian AHRs to the caecilianGymnopis multiplicata, representing the remaining extant amphibian order, Apoda.G. multiplicataAHR groups with the monophyletic vertebrate AHR/AHR1 clade. The LBD includes all three signature residues of low TCDD affinity, and a structural homology model suggests that its architecture closely resembles those of other amphibians. In transactivation assays, the EC50 for reporter gene induction by TCDD was 17.17 nM, comparable toX. laevisAhR1β (26.23 nM) andAmbystomaAHR (34.09 nM) and dramatically higher than mouse AhR (0.13 nM), a trend generally reflected in direct measures of TCDD binding. These shared properties distinguish amphibian AHRs from the high-affinity proteins typical of both more ancient vertebrate groups (teleost fish) and those that appeared more recently (tetrapods). We suggest that AHRs with low TCDD affinity represent a basal characteristic that evolved in a common ancestor of all three extant amphibian groups.

Research Highlights

A caecilian aryl hydrocarbon receptor exhibits low dioxin binding and sensitivity.

The protein’s ligand-binding domain resembles frog and salamander AHRs in structure and function.

AHR with low dioxin affinity likely evolved in a common ancestor of all three extant amphibian groups.

Graphical Abstract
Pulling the strings of cell cycle: a non-coding RNA, CcnA, modulates the master regulators CtrA and GcrA in Caulobacter crescentus
Authors: Beroual Wanassa , Prévost Karine , Lalaouna David , Zaina Nadia Ben , Valette Odile , Denis Yann , Djendli Meriem , Brasseur Gaël , Brilli Matteo , Marta Robledo Garrido , Jose-Ignacio Jimenez-Zurdo , Massé Eric , Biondi Emanuele G.
Published: September 2019

Bacteria are powerful models for understanding how cells divide and accomplish global regulatory programs. In Caulobacter crescentus, a cascade of essential master regulators supervises the correct and sequential activation of DNA replication, cell division and development of different cell types. Among them, the response regulator CtrA plays a crucial role coordinating all those functions. Here, for the first time we describe the role of a novel factor named CcnA, a cell cycle regulated ncRNA located at the origin of replication, presumably activated by CtrA and responsible for the accumulation of CtrA itself. In addition, CcnA may be also involved in the inhibition of translation of the S-phase regulator, GcrA, by interacting with its 5’ untranslated region (5’-UTR). Performing in vitro experiments and mutagenesis, we propose a mechanism of action of CcnA based on liberation (ctrA) or sequestration (gcrA) of their ribosome-binding site (RBS). Finally, its role may be conserved in other alphaproteobacterial species, such as Sinorhizobium meliloti, representing indeed a potentially conserved process modulating cell cycle in Caulobacterales and Rhizobiales.
Subpopulation identification for single-cell RNA-sequencing data using functional data analysis
Authors: Ahn Kyungmin , Fujiwara Hironobu
Published: September 2019

Background

In single-cell RNA-sequencing (scRNA-seq) data analysis, a number of statistical tools in multivariate data analysis (MDA) have been developed to help analyze the gene expression data. This MDA approach is typically focused on examining discrete genomic units of genes that ignores the dependency between the data components. In this paper, we propose a functional data analysis (FDA) approach on scRNA-seq data whereby we consider each cell as a single function. To avoid a large number of dropouts (zero or zero-closed values) and reduce the high dimensionality of the data, we first perform a principal component analysis (PCA) and assign PCs to be the amplitude of the function. Then we use the index of PCs directly from PCA for the phase components. This approach allows us to apply FDA clustering methods to scRNA-seq data analysis.

Results

To demonstrate the robustness of our method, we apply several existing FDA clustering algorithms to the gene expression data to improve the accuracy of the classification of the cell types against the conventional clustering methods in MDA. As a result, the FDA clustering algorithms achieve superior accuracy on simulated data as well as real data such as human and mouse scRNA-seq data.

Conclusions

This new statistical technique enhances the classification performance and ultimately improves the understanding of stochastic biological processes. This new framework provides an essentially different scRNA-seq data analytical approach, which can complement conventional MDA methods. It can be truly effective when current MDA methods cannot detect or uncover the hidden functional nature of the gene expression dynamics.
Saccadic foraging reveals mechanisms of value-based decision-making in primate superior colliculus
Authors: Zhang Beizhen , Kan Janis Ying Ying , Dorris Michael Christopher
Published: September 2019

Much progress has been made in understanding the neural basis of value-based decision-making using two-alternative forced-choice tasks. A limitation of these tasks is that the value of each option is often confounded with other cognitive factors (e.g. attention/choice probability/motor preparation). To overcome this limitation, monkeys were trained to use gaze to forage among many visual targets of varying value while neurophysiology was conducted in the saccade control center superior colliculus (SC). Surprisingly, each target’s value was represented in the SC predominantly in an absolute manner, that is, irrespective of the value of other available items. After fixating a target, the next choice was quickly selected once neural activity rose to a provisional ‘selection level’. This selection level systematically decreased, not as individual targets were harvested, but only after a class of value items was completely depleted. Our results reveal the exquisite balance across SC activities that transform value to choice.
The response ofPseudomonas putidato a complex lignolysate
Authors: Park Mee-Rye , Chen Yan , Thompson Mitchell , Benites Veronica T. , Fong Bonnie , Petzold Christopher J. , Baidoo Edward E. K. , Gladden John M. , Adams Paul D. , Keasling Jay D. , Simmons Blake A. , Singer Steven W.
Published: September 2019

There is strong interest in the valorization of lignin derived from plant biomass to produce valuable products; however, the structural complexity of this biopolymer has been a major bottleneck to conversion. Chemical pretreatment liberates soluble fractions of lignin that may be upgraded by biological conversion. Here, ionic liquid pretreatment was employed to obtain soluble aromatic-rich fractions from sorghum, which were converted byPseudomonas putidaKT2440, a promising host for bioconversion of aromatics derived from lignin. Growth studies and mutational analysis demonstrated thatP. putidagrowth on these soluble lignin-derived fractions, referred to as lignolysate, was dependent on aromatic monomers derived from lignin (p-coumarate and ferulate), but other, unknown factors in the lignolysate contributed to growth. Proteomic and metabolomic analyses provided evidence that these unknown factors were amino acids and residual ionic liquid. Proteomic measurements indicated a coordinated response in which these substrates were catabolized simultaneously. A cholinium catabolic pathway was identified and deletion of five genes in the pathway abrogated the ability ofP. putidato grow on cholinium as a sole carbon source. This work demonstrates that lignolysates obtained through biomass pretreatment contain multiple substrates and conversion strategies for lignin-derived should take this complexity into account.

Importance

Lignin is one of the most abundant biopolymers on Earth and is generated as a co-product in the processing of lignocellulosic biomass. Valorization of these residual lignin streams is a promising method to enhance the economic viability of modern lignocellulosic biorefineries. In this study we developed a process to couple chemical depolymerization of lignin and biological conversion usingPseudomonas putidaKT2440. Water-soluble and bioavailable lignolysate was obtained from sorghum and further characterized as a growth substrate forP. putida. Proteomic and metabolomic analyses demonstrated that P. putida metabolized other components of the lignolysate beyond monoaromatic compounds, which illuminates how microbes can process complex lignolysates obtained from plants. Understanding the underlying microbial responses in lignolysates will enable the design of rational strategies for lignin valorization.
Search as a simple take-the-best heuristic
Authors: Yahosseini Kyanoush Seyed , Moussaïd Mehdi
Published: September 2019

Humans commonly engage in a variety of search behaviours, for example when looking for an object, a partner, information, or a solution to a complex problem. The success or failure of a search strategy crucially depends on the structure of the environment and the constraints it imposes on the individuals. Here we focus on environments in which individuals have to explore the solution space gradually and where their reward is determined by one unique solution they choose to exploit. This type of environment has been relatively overlooked in the past despite being relevant to numerous real-life situations, such as spatial search and various problem-solving tasks.

By means of a dedicated experimental design, we show that the search behaviour of experimental participants can be well described by a simple heuristic model. Both in rich and poor solution spaces, a take-the-best procedure that ignores all but one cue at a time is capable of reproducing a diversity of observed behavioural patterns. Our approach, therefore, sheds lights on the possible cognitive mechanisms involved in human search.
Species-specific secretion of ESX-5 type VII substrates is determined by the linker 2 of EccC5
Authors: Bunduc C. M. , Ummels R. , Bitter W. , Houben E.N.G.
Published: September 2019

Type VII secretion systems (T7SSs) are used by mycobacteria to translocate a wide range of effector proteins across their diderm cell envelope. These systems, also known as ESX systems, have crucial roles for the viability and/or virulence of mycobacterial pathogens, including Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum. We previously observed species-specificity in the secretion of the PE_PGRS proteins by the ESX-5 system [1], in that the M. tuberculosis ESX-5 system was unable to fully complement an M. marinum esx-5 mutant. In this study, we established that the responsible factor for this is the central membrane ATPase EccC5, which has three nucleotide binding domains (NBDs). By creating chimeric M. marinum/M. tuberculosis EccC5 constructs, we observed that PE_PGRS secretion is mediated only in the presence of an EccC5 containing the cognate linker 2, irrespective of the origin of the EccC5 backbone. This region is responsible for linking the first two NBDs and for keeping the first NBD in an inhibited state. Notably, this region is disordered in a EccC crystal structure and is particularly extended in EccC proteins of the different ESX-5 systems. These results indicate that this region is involved in species-specific substrate recognition and might therefore be an additional substrate recognition site of EccC5.
GroundwaterElusimicrobiaare metabolically diverse compared to gut microbiomeElusimicrobiaand some have a novel nitrogenase paralog
Authors: Méheust Raphaël , Castelle Cindy J. , Carnevali Paula B. Matheus , Farag Ibrahim F. , He Christine , Chen Lin-Xing , Amano Yuki , Hug Laura A. , Banfield Jillian F.
Published: September 2019

Currently described members ofElusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-livingElusimicrobiahave been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associatedElusimicrobiaare predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds andRhodobacternitrogen fixation-dependent (Rnf-dependent) acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associatedElusimicrobiaoften encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and theMyxococcalesorder and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associatedElusimicrobiaclades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which someElusimicrobiaadapted to animal-associated lifestyles from free-living species via genome reduction.
A model for the regulation of the timing of cell division by the circadian clock in the cyanobacterium Synechococcus elongatus
Authors: Ho Po-Yi , Martins Bruno M.C. , Amir Ariel
Published: September 2019

1

Cells of the cyanobacterium Synechococcus elongatus possess a circadian clock in the form of three core clock proteins (the Kai proteins) whose concentrations and phosphorylation states oscillate with daily periodicity under constant conditions [1]. The circadian clock regulates the cell cycle such that the timing of cell divisions is biased towards certain times during the circadian period [2, 3, 4, 5], but the mechanism underlying how the clock regulates division timing remains unclear. Here, we propose a mechanism in which a protein limiting for division accumulates at a rate proportional to cell volume growth and modulated by the clock. This “modulated rates” model, in which the clock signal is integrated over time to affect division timing, differs fundamentally from the previously proposed “gating” concept, in which the clock is assumed to suppress divisions during a specific time window [2, 3]. We found that while both models can capture the single-cell statistics of division timing in S. elongatus, only the modulated rates model robustly places divisions away from darkness during changes in the environment. Moreover, within the framework of the modulated rates model, existing experiments on S. elongatus are consistent with the simple mechanism that division timing is regulated by the accumulation of a division limiting protein in phase with genes whose activity peak at dusk.
Transcriptomic response ofNitrosomonas europaeatransitioned from ammonia- to oxygen-limited steady-state growth
Authors: Sedlacek Christopher J. , Giguere Andrew T. , Dobie Michael D. , Mellbye Brett L. , Ferrell Rebecca V , Woebken Dagmar , Sayavedra-Soto Luis A. , Bottomley Peter J. , Daims Holger , Wagner Michael , Pjevac Petra
Published: September 2019

Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacteriumNitrosomonas europaeais the best characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology ofN. europaea, e.g. by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation onN. europaeahave focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole genome transcriptomics to investigate the overall effect of oxygen limitation onN. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia to nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper containing cytochromecoxidases encoded byN. europaeawere upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement ofN. europaea’ssNOR with regards to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase inN. europaeaand other AOB.

Importance

Nitrification is a ubiquitous, microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments increasing the eutrophication of downstream aquatic ecosystems and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their response to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here we investigate the physiology of the best characterized ammonia-oxidizing bacterium,Nitrosomonas europaea, growing under oxygen-limited conditions.
Genetic “General Intelligence,” Objectively Determined and Measured
Authors: de la Fuente Javier , Davies Gail , Grotzinger Andrew D. , Tucker-Drob Elliot M. , Deary Ian J.
Published: September 2019

It has been known for 125 years that, in humans, diverse cognitive traits are positively intercorrelated; this forms the basis for the general factor of intelligence (g). We directly test for a genetic basis for g using data from seven different cognitive tests (N = 11,263 to N = 331,679) and genome-wide autosomal single nucleotide polymorphisms. A genetic g factor accounts for 58.4% (SE = 4.8%) of the genetic variance in the cognitive traits, with trait-specific genetic factors accounting for the remaining 41.6%. We distill genetic loci broadly relevant for many cognitive traits (g) from loci associated with only individual cognitive traits. These results elucidate the etiological basis for a long-known yet poorly-understood phenomenon, revealing a fundamental dimension of genetic sharing across diverse cognitive traits.