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  1. Book ; Online: Reversible Bond Logic

    Earley, Hannah

    2023  

    Abstract: The field of molecular programming allows for the programming of the structure and behavior of matter at the molecular level, even to the point of encoding arbitrary computation. However, current approaches tend to be wasteful in terms of monomers, gate ... ...

    Abstract The field of molecular programming allows for the programming of the structure and behavior of matter at the molecular level, even to the point of encoding arbitrary computation. However, current approaches tend to be wasteful in terms of monomers, gate complexes, and free energy. In response, we present a novel abstract model of molecular programming, Reversible Bond Logic (RBL), which exploits the concepts of reversibility and reversible computing to help address these issues. RBL systems permit very general manipulations of arbitrarily complex 'molecular' structures, and possess properties such as component reuse, modularity, compositionality. We will demonstrate the implementation of a common free-energy currency that can be shared across systems, initially using it to power a biased walker. Then we will introduce some basic motifs for the manipulation of structures, which will be used to implement such computational primitives as conditional branching, looping, and subroutines. Example programs will include logical negation, and addition and squaring of arbitrarily large numbers. As a consequence of reversibility, we will also obtain the inverse programs (subtraction and square-rooting) for free. Due to modularity, multiple instances of these computations can occur in parallel without cross-talk. Future work aims to further characterize RBL, and develop variants that may be amenable to experimental implementation.

    Comment: 22 pages, 10 figures
    Keywords Computer Science - Emerging Technologies
    Publishing date 2023-05-12
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: The $\aleph$-Calculus

    Earley, Hannah

    A declarative model of reversible programming

    2022  

    Abstract: A novel model of reversible computing, the $\aleph$-calculus, is introduced. It is declarative, reversible-Turing complete, and has a local term-rewriting semantics. Unlike previously demonstrated reversible term-rewriting systems, it does not require ... ...

    Abstract A novel model of reversible computing, the $\aleph$-calculus, is introduced. It is declarative, reversible-Turing complete, and has a local term-rewriting semantics. Unlike previously demonstrated reversible term-rewriting systems, it does not require the accumulation of history data. Terms in the $\aleph$-calculus, in combination with the program definitions, encapsulate all program state. An interpreter was also written.

    Comment: 7 pages, 1 listing, 14th Conference on Reversible Computation
    Keywords Computer Science - Programming Languages
    Publishing date 2022-06-13
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Timing of Low Molecular Weight Heparin Administration in Breast Surgery and Post-Operative Haematoma Formation.

    Fullard, A / Earley, H / Lowery, A / Lal, A / Merrigan, A / Tormey, S

    Irish medical journal

    2020  Volume 113, Issue 4, Page(s) 54

    Abstract: Aims The aims of this study were to: identify current practice regarding low molecular weight heparin (LMWH) prophylaxis in elective breast surgery, to determine if timing of administration of LMWH prophylaxis or specific patient demographic factors ... ...

    Abstract Aims The aims of this study were to: identify current practice regarding low molecular weight heparin (LMWH) prophylaxis in elective breast surgery, to determine if timing of administration of LMWH prophylaxis or specific patient demographic factors impacts the rate of post-operative haematoma formation. Methods Retrospective cohort study involving 100 patients who underwent elective breast surgery in a tertiary centre in Ireland in 2017. Medical charts were reviewed to collect data on; timing of LMWH administration, incidence of post-operative haematoma and patient's age, BMI, smoking status and anti-coagulant use. Statistical analysis was then performed. Results Forty-two patients (42%) received enoxaparin pre-operatively and thirty-one patients (31%) post-operatively. Incidence of post-operative haematoma was 4% (n=4). Of the haematoma group, three patients (75%) received post-operative enoxaparin (p=0.166). Independent patient factors did not significantly impact rate of haematoma formation. Conclusions Post-operative haematoma rate is 4%. Timing of LMWH prophylaxis administration did not significantly affect this rate.
    MeSH term(s) Breast/surgery ; Breast Diseases/surgery ; Elective Surgical Procedures ; Female ; Hematoma/epidemiology ; Hematoma/prevention & control ; Heparin, Low-Molecular-Weight/administration & dosage ; Humans ; Mastectomy ; Middle Aged ; Perioperative Care ; Postoperative Complications/epidemiology ; Postoperative Complications/prevention & control ; Postoperative Hemorrhage/prevention & control ; Retrospective Studies ; Thromboembolism/prevention & control ; Time Factors
    Chemical Substances Heparin, Low-Molecular-Weight
    Language English
    Publishing date 2020-04-03
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 193134-9
    ISSN 0332-3102 ; 0021-129X
    ISSN 0332-3102 ; 0021-129X
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    Zs.B 148: Show issues Location:
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  4. Article: A fundamental change emerging in locally advanced rectal cancer management: a case report.

    Edwards-Murphy, Amy / Earley, Helen / Creavin, Ben / McCullough, Peter / Cooke, Fiachra / Neary, Peter

    Journal of surgical case reports

    2022  Volume 2022, Issue 9, Page(s) rjac405

    Abstract: Treatment of locally advanced rectal cancer remains a challenge in colorectal surgery. It has had an evolving landscape over the past three decades. Implementation of total neoadjuvant therapy (TNT) as a novel approach to management has begun globally ... ...

    Abstract Treatment of locally advanced rectal cancer remains a challenge in colorectal surgery. It has had an evolving landscape over the past three decades. Implementation of total neoadjuvant therapy (TNT) as a novel approach to management has begun globally but long-term outcomes and data analysis to identify optimal schedules are eagerly awaited. We report a case of locally advanced rectal cancer management in a young male with a complete pathological response to TNT.
    Language English
    Publishing date 2022-09-19
    Publishing country England
    Document type Case Reports
    ZDB-ID 2580919-2
    ISSN 2042-8812
    ISSN 2042-8812
    DOI 10.1093/jscr/rjac405
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  5. Article ; Online: A palliative stent for an acute large bowel obstruction-A video vignette.

    Edwards Murphy, Amy / Earley, Helen / Creavin, Ben / McCullough, Peter / Cooke, Fiachra / Neary, Peter

    Journal of surgical oncology

    2022  Volume 127, Issue 3, Page(s) 441

    MeSH term(s) Humans ; Intestinal Obstruction/etiology ; Intestinal Obstruction/surgery ; Colonic Diseases ; Stents ; Palliative Care ; Colorectal Neoplasms ; Treatment Outcome
    Language English
    Publishing date 2022-11-01
    Publishing country United States
    Document type Video-Audio Media ; Journal Article
    ZDB-ID 82063-5
    ISSN 1096-9098 ; 0022-4790
    ISSN (online) 1096-9098
    ISSN 0022-4790
    DOI 10.1002/jso.27133
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    Zs.A 706: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  6. Article ; Online: Colonisation of the colonic mucus gel layer with butyrogenic and hydrogenotropic bacteria in health and ulcerative colitis.

    Earley, Helen / Lennon, Grainne / Coffey, J Calvin / Winter, Desmond C / O'Connell, P Ronan

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 7262

    Abstract: Butyrate is the primary energy source for colonocytes and is essential for mucosal integrity and repair. Butyrate deficiency as a result of colonic dysbiosis is a putative factor in ulcerative colitis (UC). Commensal microbes are butyrogenic, while ... ...

    Abstract Butyrate is the primary energy source for colonocytes and is essential for mucosal integrity and repair. Butyrate deficiency as a result of colonic dysbiosis is a putative factor in ulcerative colitis (UC). Commensal microbes are butyrogenic, while others may inhibit butyrate, through hydrogenotropic activity. The aim of this study was to quantify butyrogenic and hydrogenotropic species and determine their relationship with inflammation within the colonic mucus gel layer (MGL). Mucosal brushings were obtained from 20 healthy controls (HC), 20 patients with active colitis (AC) and 14 with quiescent colitis (QUC). Abundance of each species was determined by RT-PCR. Inflammatory scores were available for each patient. Statistical analyses were performed using Mann-Whitney-U and Kruskall-Wallis tests. Butyrogenic R. hominis was more abundant in health than UC (p < 0.005), prior to normalisation against total bacteria. Hydrogenotropic B. wadsworthia was reduced in AC compared to HC and QUC (p < 0.005). An inverse correlation existed between inflammation and R. hominis (ρ - 0.460, p < 0.005) and B. wadsworthia (ρ - 0.646, p < 0.005). Other hydrogenotropic species did not widely colonise the MGL. These data support a role for butyrogenic bacteria in UC. Butyrate deficiency in UC may be related to reduced microbial production, rather than inhibition by microbial by-products.
    MeSH term(s) Adult ; Aged ; Bilophila/metabolism ; Butyrates/metabolism ; Clostridiales/metabolism ; Colitis, Ulcerative/microbiology ; Colon/microbiology ; Female ; Humans ; Intestinal Mucosa/microbiology ; Male ; Middle Aged
    Chemical Substances Butyrates
    Language English
    Publishing date 2021-03-31
    Publishing country England
    Document type Clinical Trial ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-86166-6
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  7. Article: A dramatic reduction in surgical consults in a University Teaching Hospital during the COVID-19 pandemic.

    Connelly, Tara M / Bass, Gary A / Earley, Helen / Umair, Muhammad / O'Riordan, James

    The surgeon : journal of the Royal Colleges of Surgeons of Edinburgh and Ireland

    2020  Volume 19, Issue 2, Page(s) e40–e41

    MeSH term(s) COVID-19/epidemiology ; Comorbidity ; Hospitals, University/statistics & numerical data ; Humans ; Infection Control/methods ; Pandemics ; Referral and Consultation/statistics & numerical data ; Surgical Procedures, Operative/statistics & numerical data
    Keywords covid19
    Language English
    Publishing date 2020-08-01
    Publishing country Scotland
    Document type Letter
    ZDB-ID 2102927-1
    ISSN 1479-666X
    ISSN 1479-666X
    DOI 10.1016/j.surge.2020.07.010
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    Zs.A 5756: Show issues Location:
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  8. Article ; Online: Deadly combination:

    Cullinane, Carolyn / Earley, Helen / Tormey, Shona

    BMJ case reports

    2017  Volume 2017

    Abstract: Gas gangrene is a life-threatening, necrotising soft tissue infection. Colorectal malignancy- ... ...

    Abstract Gas gangrene is a life-threatening, necrotising soft tissue infection. Colorectal malignancy-associated
    MeSH term(s) Aged ; Clostridium septicum ; Colorectal Neoplasms/microbiology ; Gas Gangrene/microbiology ; Humans ; Male
    Language English
    Publishing date 2017-12-02
    Publishing country England
    Document type Case Reports ; Journal Article
    ISSN 1757-790X
    ISSN (online) 1757-790X
    DOI 10.1136/bcr-2017-222759
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  9. Article ; Online: Outcomes After Colonic Self-Expanding Metal Stent Insertion Without Fluoroscopy: A Surgeon-Led 10-Year Experience.

    Connelly, Tara M / Ryan, Jessica / Foley, Niamh M / Earley, Helen / Sahebally, Shaheel M / O'Brien, Carl / McCullough, Peter / Neary, Peter / Cooke, Fiachra

    The Journal of surgical research

    2022  Volume 281, Page(s) 275–281

    Abstract: Introduction: Colonic self-expanding metal stents (SEMS) can be used to relieve malignant and benign large bowel obstruction (LBO) as a bridge to surgery (BTS) and for palliation. Guidelines suggest the use of fluoroscopic guidance for deployment. This ... ...

    Abstract Introduction: Colonic self-expanding metal stents (SEMS) can be used to relieve malignant and benign large bowel obstruction (LBO) as a bridge to surgery (BTS) and for palliation. Guidelines suggest the use of fluoroscopic guidance for deployment. This may be difficult to obtain after hours and in certain centers. We aimed to determine the outcomes of stenting under endoscopic guidance alone.
    Methods: All patients who underwent SEMS insertion in our tertiary referral center between August 2010 and June 2021 were identified from a prospectively maintained database. Patient demographics (age/gender), disease characteristics (benign versus malignant/location/stage), stenting intent (BTS versus palliative), and outcomes (technical success/stoma/time from stenting to resection/death/study end) were analyzed.
    Results: Fifty-three (n = 39, 73.6% male) patients underwent SEMS insertion. Indications included colorectal carcinoma (n = 48, 90.6%), diverticular stricture (n = 3), and gynecological malignancy (n = 2). In five (9.4%) patients (four BTS and one palliative), SEMSs deployment was not completed because of the inability to pass the guidewire. All underwent emergency surgery. In the BTS cohort (n = 29, median 70.4 [range 40.3-91.8] years), 10 patients underwent neoadjuvant chemoradiotherapy. The permanent stoma rate was 20.7% (n = 6). There was no 30- or 90-d mortality. In the palliative cohort (n = 24, median age 77.1 [range 54.4-91.9]), 16 (66.7%) were deceased at the study end. The median time from stenting to death was 5.2 (2.3-7.9) months.
    Conclusions: SEMS placed under endoscopic visualization alone, palliatively and as a BTS, had acceptable stoma, morbidity, and mortality rates. These results show that SEMS insertion can be safely performed without fluoroscopy.
    MeSH term(s) Humans ; Male ; Aged ; Female ; Treatment Outcome ; Retrospective Studies ; Intestinal Obstruction/etiology ; Intestinal Obstruction/surgery ; Stents/adverse effects ; Colorectal Neoplasms/pathology ; Palliative Care/methods ; Fluoroscopy/adverse effects ; Surgeons ; Colonic Diseases/etiology ; Colonic Diseases/surgery
    Language English
    Publishing date 2022-10-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 80170-7
    ISSN 1095-8673 ; 0022-4804
    ISSN (online) 1095-8673
    ISSN 0022-4804
    DOI 10.1016/j.jss.2022.08.043
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    Zs.A 178: Show issues Location:
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  10. Article: A dramatic reduction in surgical consults in a University Teaching Hospital during the COVID-19 pandemic

    Connelly, Tara M / Bass, Gary A / Earley, Helen / Umair, Muhammad / O039, / Riordan, James

    Surg. (Edinb.)

    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #765655
    Database COVID19

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