bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Emergent Self-Organizing Map Based Analysis Pipeline for	Comparative Metabolome Studies
Authors: Haddad Isam , Hiller Karsten , Frimmersdorf Eliane , Benkert Beatrice , Schomburg Dietmar , Jahn Dieter 
Published: December 2019

Modern high-throughput techniques allow for the identification and quantification of hundreds of metabolites of a biological system which cover central parts of the metabolome. Due to the amount and complexity of obtained data there is an increasing need for the development of appropriate computational interpretation methods. A novel data analysis pipeline designed for high-throughput determined metabolomic data is presented. The combination of principal component analysis (PCA) with emergent self-organizing maps (ESOM) and hierarchical cluster analysis (HCA) algorithms is used to unravel the structure underlying metabolomic data sets, including the detection of outliers. Observed differences between various analyzed metabolomes are automatically mapped and visualized using KEGG metabolic pathway maps. This way typical metabolic biomarker for data sets from various analyzed growth conditions and genetic backgrounds become visible. In order to validate the described methods we analyzed time resolved metabolomic datasets obtained for Corynebacterium glutamicum cells grown on various carbon sources consisting of 126 different metabolic patterns. The analysis pipeline was implemented in the user-friendly Java software eSOMet. The software was successfully used for the clustering of the metabolome data mentioned above. Metabolic biomarkers typical for the utilized carbon sources and analyzed growth phases were identified.
A Concept for ab initio Prediction of cis-regulatory Modules
Authors: Ecker K. , Welch L. 
Published: December 2019

An important concern in the attempt of understanding the functional code of eukaryotic genes is to elucidate the control structures for regulating gene activation and suppression. One objective in the attempt to understand mechanisms of gene regulation is the elucidation of the regulatory network structure. A preliminary step of a detailed network analysis is identifying the transcription factor binding sites of a regulatory network. Known as cis-regulatory module (CRM), it is understood as part of the genome that comprises a set of short length binding sites. Gene regulatory systems are known to be quite stable during evolution, as compared to relatively frequent replication processes of genes and mutations of the coding sequences. This conservation property of regulatory code can advantageously be used for identifying cis-regulatory modules of potentially co-regulated genes. As the degree of similarity is expected to depend on the phylogenetic distance of homologs or orthologs, we favor an approach that is based on a comparison paradigm. The paper introduces a novel concept for measuring the similarity of cis-regulatory modules which can then be used in an algorithm for comparing regulatory regions. The proposed algorithm searches for pairs of similar modules, and a prototype implementation is applied to human and mouse liver sequences. The results are compared to that of random sequences, and it is shown that a clear decision about co-regulation is possible at this level.
A decentralized and self organizing architecture for wide area synchronized monitoring of smart grids
Authors: Formato Giuseppina , Loia Vincenzo , Paciello Vincenzo , Vaccaro Alfredo 
Published: December 2019

Synchronized Wide-Area Monitoring Systems (WAMS) involve the use of power system-wide measurements to avoid large disturbances and reduce the probability of catastrophic events. In these systems a large volume of raw data is collected by distributed sensors and sent to central servers for post processing activities. Many research works conjectured that this hierarchical monitoring paradigm could be not affordable in addressing the increasing network complexity and the massive data exchanging characterizing modern smart grids. Unaffordable complexity, hardware redundancy, network bandwidth and data storage resources are the main barriers imposed by technology and costs. Moreover, in WAMS the global absolute time reference for sensors synchronization is typically obtained by satellite-based timing signals processing. Since these signals are extremely vulnerable to radiofrequency interference (i.e. cyber-attacks), effective countermeasures aimed at increasing the resilience of synchronized WAMS to external and internal interferences need to be designed. In trying and addressing these challenges, in this paper the role of decentralized consensus protocols for decentralized and synchronized wide area smart grids monitoring is analyzed.
An efficient and dependable protocol for critical MANETs
Authors: Elgohary Ashraf , Sobh Tarek S. , Nouh Sayed A. , Zaki M. 
Published: December 2019

Critical MANET environments such as military battlefields and disaster recovery operations impose a number of requirements such as the need for robustness and performance within high mobility scenarios; also, they impose some constraints such as Hostile attacks, RF range and cost, battery limitations. We studied the core-based routing protocol PUMA, in addition to two ant-based routing protocols MANHSI and AAMRP to identify their drawbacks while working in critical MANETs. Finally, we propose a novel routing protocol named Adaptive Secure Headship Following Induction Keeping (ASHFIK) to work ideally in critical MANETs scenarios. In this paper, we discuss the structure of ASHFIK, which uses a new mechanism called the Headship Mechanism, which provides always a standby core to work if the original core is down. After studying performance analysis of ASHFIK compared to PUMA, we can conclude that ASHFIK is particular suitable for most critical MANETs scenarios.
A high-performance QoS-enhanced proportional fair scheduling algorithm over downlink OFDMA-based networks
Authors: Chao I-Fen , Chiou Chuei-Sheng 
Published: December 2019

OFDMA-based networks have been considered to be a promising solution to wireless networks especially for broadband multimedia mobile services. The major challenges pertaining to such OFDMA-based networks are to design a medium access control scheme that is expected to exploit multi-channel multi-rate diversity and with QoS provision. The previous existing scheduling algorithms either target at maximizing system throughput while starving the low-rate users, or focus on throughput fairness but seriously decreasing the system throughput. While proportional fair (PF) has emerged as a prominent candidate in wireless networks, as it achieves a good tradeoff between system throughput and fairness, PF still leads to low throughput of bad channel users, resulting in limiting the attainable QoS throughput for the entire system. In this paper, we propose a QoS-enhanced proportional fair (QEPF) scheduling algorithm, which aims at maximizing QoS throughput while still retaining fairness as well as maximizing system throughput in downlink OFDMA networks. QEPF proposes a QoS-enhanced PF-based utility function, which supports QoS and is a low-complexity algorithm for multi-channel OFDMA networks. We demonstrate via extensive simulation results, that QEPF outperforms PF in terms of system throughput and mean delay. The results illustrate that QEPF surprisingly attains great performance for poor channel users, while not sacrifices the performance of good channel users. Furthermore, the results show that QEPF well accommodates nearly twice the amount of high priority data than PF does.
A Set of Multicast Primitives for Fault Tolerant Distributed Systems
Authors: Pagani Elena , Rossi Gian Paolo 
Published: December 2019

Reliable multicast among the members of a group is recognized as an important service to support emerging multimedia and distributed applications, These applications have a variety of multicast requirements that may be matched with the semantics of the multicast primitives provided by an underlying layer. This paper deals with the design and the implementation of a high level set of multicast primitives that combine both message ordering and message atomicity semantics. The primitives provide uniform agreement in a synchronous environment in which both omission and crash failures may occur. We introduce a novel algorithmic approach through which the normal processing of the messages can be performed together with the recovery actions that are required to cope with failures. As a consequence, under failure conditions the algorithms perform better in terms of both network load and throughput. Nonetheless, a comparable behaviour under reliable conditions is ensured. Furthermore, by using a stable storage as part of the fault tolerance method, the algorithms autonomously distinguish amongst permanent (crashes) or transient (omission) failures. This makes them independent of the underlying transport service and adaptable to different protocol suites. The paper also contains the analysis of the performances obtained from the initial implementation of the described primitives.
Survey results from a national survey of community rehabilitation	providers holding special wage certificates
Authors: Inge Katherine J. , Wehman Paul , Revell Grant , Erickson Doug , Butterworth John , Gilmore Dana 
Published: December 2019

The purpose of this paper is to present the findings from a national survey of a random sample of community rehabilitation programs (CRPs) that hold Special Wage Certificates established under Section 14(c) of the Fair Labor Standards Act (FLSA), 29 U.S.C. 214(c). The intent of the survey was to identify the types of services provided, the trends in the employment services, and the factors that were perceived as inhibiting and facilitating integrated employment outcomes. The survey results are categorized for this report in the following three areas: 1) characteristics of community rehabilitation programs, 2) organizational change trends, and 3) factors that influence the type of employment program utilized by consumers with disabilities. Representative results from the survey are that overall, facility-based programs continue to be the predominant service provided by community rehabilitation programs holding 14(c) certificates. Of the 20,075 staff members identified as serving consumers, only 1,741 (8.7% are reported as working with individuals earning at least minimum wage. Although competitive employment and individual supported employment services among these CRPs are growing at a faster rate than other services, use of facility-based services continues to expand. Overall, the findings indicate that the organizations that provide daily services to those Americans with disabilities utilizing 14(c) certificates are continuing to predominately support facility-based work and non-work activities versus services leading to integrated employment outcomes.
Effects of beractant and poractant administration on cerebral	hemodynamics
Authors: Fujii Alan M. , Bailey Jennifer , Doros Gheorghe , Sampat Kunal , Sikes N. Carol , Mason Melanie J. , Kaiser Jeffrey R. 
Published: December 2019

Objective: To determine whether type and timing of surfactant preparation affect cerebral blood flow (CBF) hemodynamics differently. Study design: Two sites monitoring cerebral hemodynamics during surfactant administration. Beractant (4.0 ml/kg) and poractant (2.5 ml/kg first dose, 1.25 ml/kg subsequent doses) were administered according to the manufacturer. CBF velocity (CBFv) was assessed before and after the first (Site A) and second (Site B) doses of beractant and poractant. Results: At Site A, 10 infants (birth weight 690 ± 133 g) were studied. CBFv decreased 28.9 ± 5.1% following the first dose of surfactant; there were no differences between beractant and poractant. At Site B, 16 infants (birth weight 896 ± 311 g) were studied. CBFv increased 47.4 ± 35.7% after the second dose of beractant and did not change after the second dose of poractant. Conclusion: This is a preliminary report of two related trials examining CBFv responses to beractant and poractant. CBFv decreased similarly after the first dose of beractant and poractant. CBFv increased after the second dose of beractant, but not after poractant. Cerebral hemodynamic responses between the first and second doses may be due to differences in quantities of airway fluid, while second dose differences between beractant and poractant may be due to differences in dose-volume.
Maternal serum selenium and low birth weight neonates
Authors: Mohammadzadeh A. , Farhat A.S. , Valaee L. , Khadem N. , Khajedaluee M. , Parizadeh S.M.R. 
Published: December 2019

Introduction: Selenium is an essential element for the protection against oxidative stress in different biological materials. Excessive or insufficient intake of selenium can lead to clinically relevant disturbances in tissue functions. Selenium status is particularly important for neonates, and infants. Therefore, the aim of this prospective study was to examine the relationship between the concentration of serum selenium in pregnant women and the incidence of low birth weight (< 2500 g) in their newborns. Method: We conducted a case-control study on women who delivered low birth weight infants (Cases), and women with normal birth weight infants (Controls). We collected blood samples from all women within 24 hours of delivery, and assessed the concentration of selenium using electrothermal atomic absorption spectrometry. We compared serum concentration of selenium between the two groups. Multiple linear regression analysis was performed to control of potential confounding variables. Results: A total of 123 mothers were studied, of them 70 Cases with low birth weight infants (1845 ± 472 g) and 53 Controls (birth weight = 3166 ± 435 g). Mothers in the Cases and Controls groups did not differ in age (24 ± 4 vs. 24.7 ± 5.4 years), body mass index (23.4 ± 3.4 vs. 22.9 ± 3.2), and socioeconomic or demographic factors. Maternal selenium concentration (μg/l) did not differ between Cases and Controls; 118.8 ± 24.5 μg/l vs. 122.5 ± 29.3 μg/l respectively. Maternal selenium did not differ between premature and full term deliveries. Small for gestational age and appropriate for gestational age newborns had similar maternal selenium concentrations. Conclusion: In our study population, maternal selenium concentration had no impact on neonatal birth weights or premature deliveries.
Comparison of pigtail percutaneous versus traditional chest tube	thoracotomy for pneumothorax drainage in neonates
Authors: Molloy Eleanor J. , Walsh M.C. 
Published: December 2019

Objective: Pigtail seldinger "over the wire" technique chest drains have been shown to be as effective and less invasive in adults than traditional chest tube thoracotomy. We aimed to compare conventional and pigtail chest tube management of pneumothorax in neonates. Methods: Retrospective comparison of pigtail and conventional chest tubes in neonates with pneumothorax in a tertiary neonatal intensive care unit. Results: 28 chest tubes were inserted in 18 neonates (23–39 weeks) including 12 conventional and 16 pigtail chest drains. Significantly increased analgesia was required while conventional chest drains were in situ compared to pigtail tubes. In addition 6 pneumothoraces were unresolved with conventional drains versus 1 following pigtail drain insertion. Conclusion: Optimising management of acute pneumothorax would improve neonatal morbidity and mortality. The use of the smaller and more flexible pigtail thoracostomy may minimise lung injury during insertion and decrease analgesia requirements
Orogastric tube placement in extremely low birth weight	infants
Authors: Cordero Leandro , Nankervis Craig A. , Coley Brian D. , Giannone Peter J. 
Published: December 2019

Background: Traditionally, orogastric tube (OGt) length of insertion is determined by nose-earlobe-xyphoid (NEX) measurement. Although radiography is the gold standard for verification of placement, scarce data are available for extremely low birth weight (ELBW) infants. Objective: To correlate OGt placement in ELBW infants with its position in the gastrointestinal tract by radiography and to establish clinical correlates with gastrointestinal perforations. Design/methods: Retrospective evaluation of 290 ELBW infants. The 1st (n=290) and 2nd (n=273) radiographs following OGt placement were evaluated. Diaphragm and OGt were referenced to the level of the 10{th} thoracic vertebra (T10). The lower esophageal sphincter (LES) was presumed to be at T9. Results: Most (86%) OGt were placed during the first three days of life. OGt pores and the stomach were visible in 37% and 40% of the cases respectively. The diaphragm was noted to be at T8 (14%), T9 (43%), T10 (41%) & T11 (2%). On the first radiograph, OGt were in the esophagus (4%), in the duodenum (3%), straight in the stomach (8%) and diagonal in the stomach (85%). Of all 563 radiographs evaluated, 502 (89%) OGt were diagonal in the stomach, extending below the LES for a median 3 cm (0.7–4.9 cm). In the 225 radiographs where the stomach could be visualized, the median distance from T10 to the OGt tip was 2.8 cm (1–5) while that from T10 to the greater curvature was 3.1 cm (1–5). Clinical correlates: There were 21 cases of necrotizing enterocolitis (15 of them with perforation) and 7 cases of spontaneous intestinal perforation. None of them were temporally or anatomically linked to OGt placement. Conclusions: Radiological verification of OGt placement is possible. The unpredictable level of the diaphragm, the poor visibility of OGt pores and the often gasless stomach can make radiological verification difficult. Determining OGt insertion length in ELBW infants by the NEX method results in appropriate intragastric placement in 85% of the cases.
Predictors of medical failure in the preterm patent ductus	arteriosus
Authors: Awad Sawsan M. , Khalid Omar , Suarez William 
Published: December 2019

Background: The management of the patent ductus arteriosus in the preterm neonate continues to be a major factor affecting morbidity and mortality. Objectives: To identify factors that may be important in determining which patients respond to medical therapy and which would suggest that surgical management is likely necessary. Methods: A total of 117 patients' charts were retrospectively reviewed. Twenty-two were excluded due to incomplete data. Ninety-five patients were divided into medical responders (R) and non-responders (NR). Demographics and clinical data were compared using independent t-testing and ANOVA. A Ductal Response Score (DRS) was developed using factors known to be of significance for successful medical closure. This score was calculated on a subset of patients where all necessary data were present. Results: Responders had higher gestational age (GA), body surface area (BSA) and left ventricular Z-score (LVZ-score). The interaction between groups showed significant difference between R and NR in LA/AO (P < 0.001), LV Z-score (P < 0.001), and BUN/Cr (P = 0.046), where NR had higher values compared to R. The effect of time on the DRS regardless of the group (10 patients) showed statistically insignificant difference (P= 0.263). Interaction between the groups (R = 6, NR = 4) showed significant worsening of the DRS in NR (P = 0.047). Extrapolation of data was performed. Independent t-test on DRS between groups, post-extrapolation (R = 19, NR = 9), showed statistically insignificant difference between the groups (P = 0.144). Conclusion: The concept of determining a DRS may prove to be useful in evaluating response to medical therapy. However, further prospective study is needed.
A simplified method for head cooling: Feasibility and safety
Authors: AlKharfy Turki M. 
Published: December 2019

Objective: To study feasibility of a simplified method of head cooling using ice water filled rubber gloves in full term infants with moderate to severe hypoxic-ischemic encephalopathy and whether very early induced hypothermia would decrease mortality and incidence of convulsions in this group of infants. Study Design: In this single center prospective cohort study, full term inborn infants were assigned to intervention cohort or control cohort based on the 24 hours on call staff physician preference. Patient selection was based on perinatal evidence of hypoxic-ischemic insult and clinical neurological findings on admission suggestive of moderate to severe hypoxic-ischemic encephalopathy. Hypothermia was passively initiated at delivery and was actively induced on admission. A simplified approach to induced head cooling was used by applying ice water filled rubber gloves. Combined selective head cooling and mild systemic hypothermia approach was applied. Cooling was continued for 72 hours. Short term outcomes of infants in the two cohorts were compared. Results: 106 infants were enrolled, 54 infants in intervention cohort and 52 infants in control cohort. Active cooling was initiated in the intervention cohort at a median postnatal age of 57 minutes. The method of cooling was easy to learn and adopt by our unit members. The mortality rate was not significantly different between the two cohorts; 8/54 intervention cohort vs. 11/52 in the control cohort, p value 0.45. Infants in the intervention cohort had statistically significant reduction in the incidence of clinical convulsions, 14/54 vs. 25/52, p value 0.026. Fewer infants in the intervention group had abnormal electroencephalogram; 12/46 (26%) vs. 18/43 (42%) in the control group, however this did not reach statistical significance. Conclusion: This simplified method of head cooling is feasible and might be helpful to treat newborn infants with hypoxic-ischemic encephalopathy in centers where sophisticated equipments are not available.
Pneumatosis coli: A benign form of necrotizing enterocolitis
Authors: Cordero Leandro , Giannone Peter J. , Valentine Christina J. , Coley Brian D. , Nankervis Craig A. 
Published: December 2019

Background: Recently, we observed an increase in the number of late preterm neonates with pneumatosis coli (Pcoli) an infrequently reported benign form of necrotizing enterocolitis (NEC). Objective: To review our experience (2000–09) with infants who presented with visible blood in the stools (VBS) and pneumatosis intestinalis (PI). Methods: Retrospective cohort study. There were 65~infants who had VBS and PI. Thirty-two who constituted the pneumatosis coli (Pcoli) group were compared with 33 infants with VBS and PI who were designated as classic NEC. Results: 75% of Pcoli cases occurred during 2008–09. Demographics and obstetrical risk factors (except for preterm labor and antepartum steroid use) for the mothers of both groups were similar. Ninety-one percent of Pcoli were $\geq $ 34w while 82% of classic NEC cases were ⩽ 33w GA. At the time of diagnosis 70% of infants in the Pcoli group and 30% of those in the classic NEC group were < 7d old. In the Pcoli group prior to VBS, 78% of these infants were taking formula and 22% formula and breast milk. VBS was the only clinical sign which prompted radiographic evaluation. Thirty of these 32 infants had blood cultures (all negative), 20% received antibiotics, 50% continued with feedings, no patients had surgery and all survived. In the classic NEC group prior to VBS 47% were taking formula, 47% formula and breast milk and 6% breast milk. Seventy-four percent of these infants had abdominal distention, emesis or apnea, 48% had abnormal WBC-diff, and 6 infants had positive blood cultures. Ten infants had surgery and 3 of them expired. Among Pcoli infants, PI was limited to the colon in 94% of the cases. In the classic NEC group 35% of infants had difuse PI, 65% had focal PI and 27% had portal venous gas. Conclusion: Pcoli is a benign form of NEC that affects mainly late preterm or term infants, who once diagnosed, in contrast to classic NEC patients, require less intensive care. Further studies are needed to elucidate etiology (including the role of feeding practices) and to explore preventive or therapeutic measures.